rs939885

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_152672.6(SLC51A):c.604G>A(p.Val202Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 1,613,134 control chromosomes in the GnomAD database, including 188,626 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.43 ( 15257 hom., cov: 32)

Exomes 𝑓: 0.48 ( 173369 hom. )

Consequence

SLC51A
NM_152672.6 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.0890

Publications

41 publications found

Variant links:

Genes affected

SLC51A (HGNC:29955): (solute carrier family 51 member A) Predicted to enable protein heterodimerization activity; protein homodimerization activity; and transmembrane transporter activity. Involved in bile acid secretion. Located in basolateral plasma membrane. Implicated in progressive familial intrahepatic cholestasis. [provided by Alliance of Genome Resources, Apr 2022]

SLC51A links:

PCYT1A (HGNC:8754): (phosphate cytidylyltransferase 1A, choline) This gene belongs to the cytidylyltransferase family and is involved in the regulation of phosphatidylcholine biosynthesis. Mutations in this gene are associated with spondylometaphyseal dysplasia with cone-rod dystrophy. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2015]

PCYT1A Gene-Disease associations (from GenCC):

spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), ClinGen, Orphanet
Leber congenital amaurosis
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

PCYT1A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.1412093E-6).

BP6

Variant 3-196228891-G-A is Benign according to our data. Variant chr3-196228891-G-A is described in ClinVar as Benign. ClinVar VariationId is 3059296.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC51A	NM_152672.6 link	c.604G>A	p.Val202Ile	missense_variant	Exon 6 of 9	ENST00000296327.10	NP_689885.4	Q86UW1
SLC51A	XM_047447662.1 link	c.256G>A	p.Val86Ile	missense_variant	Exon 5 of 8		XP_047303618.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC51A	ENST00000296327.10 link	c.604G>A	p.Val202Ile	missense_variant	Exon 6 of 9	1	NM_152672.6	ENSP00000296327.5		Q86UW1

Frequencies

GnomAD3 genomes

AF:

0.428

AC:

65047

AN:

151850

Hom.:

15243

Cov.:

show subpopulations

Gnomad AFR

AF:

0.242

Gnomad AMI

AF:

0.396

Gnomad AMR

AF:

0.550

Gnomad ASJ

AF:

0.500

Gnomad EAS

AF:

0.755

Gnomad SAS

AF:

0.417

Gnomad FIN

AF:

0.434

Gnomad MID

AF:

0.453

Gnomad NFE

AF:

0.485

Gnomad OTH

AF:

0.460

GnomAD2 exomes

AF:

0.488

AC:

122599

AN:

251448

AF XY:

0.484

show subpopulations

Gnomad AFR exome

AF:

0.232

Gnomad AMR exome

AF:

0.576

Gnomad ASJ exome

AF:

0.498

Gnomad EAS exome

AF:

0.764

Gnomad FIN exome

AF:

0.437

Gnomad NFE exome

AF:

0.483

Gnomad OTH exome

AF:

0.485

GnomAD4 exome

AF:

0.482

AC:

703960

AN:

1461166

Hom.:

173369

Cov.:

AF XY:

0.480

AC XY:

348732

AN XY:

726908

show subpopulations

African (AFR)

AF:

0.236

AC:

7894

AN:

33472

American (AMR)

AF:

0.569

AC:

25469

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.492

AC:

12870

AN:

26132

East Asian (EAS)

AF:

0.779

AC:

30937

AN:

39694

South Asian (SAS)

AF:

0.407

AC:

35124

AN:

86240

European-Finnish (FIN)

AF:

0.429

AC:

22925

AN:

53414

Middle Eastern (MID)

AF:

0.453

AC:

2612

AN:

5766

European-Non Finnish (NFE)

AF:

0.484

AC:

537650

AN:

1111358

Other (OTH)

AF:

0.472

AC:

28479

AN:

60368

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

18440

36880

55320

73760

92200

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15882

31764

47646

63528

79410

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.428

AC:

65092

AN:

151968

Hom.:

15257

Cov.:

AF XY:

0.434

AC XY:

32209

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.243

AC:

10054

AN:

41456

American (AMR)

AF:

0.550

AC:

8389

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

1732

AN:

3464

East Asian (EAS)

AF:

0.756

AC:

3899

AN:

5158

South Asian (SAS)

AF:

0.417

AC:

2007

AN:

4808

European-Finnish (FIN)

AF:

0.434

AC:

4584

AN:

10554

Middle Eastern (MID)

AF:

0.452

AC:

133

AN:

294

European-Non Finnish (NFE)

AF:

0.485

AC:

32953

AN:

67948

Other (OTH)

AF:

0.464

AC:

980

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1774

3548

5321

7095

8869

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

608

1216

1824

2432

3040

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.478

Hom.:

59458

Bravo

AF:

0.433

TwinsUK

AF:

0.491

AC:

1819

ALSPAC

AF:

0.497

AC:

1917

ESP6500AA

AF:

0.247

AC:

1089

ESP6500EA

AF:

0.478

AC:

4108

ExAC

AF:

0.477

AC:

57910

Asia WGS

AF:

0.548

AC:

1904

AN:

3478

EpiCase

AF:

0.492

EpiControl

AF:

0.492

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

SLC51A-related disorder

Benign:1

Jun 22, 2023

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.054

BayesDel_addAF

Benign

-0.80

BayesDel_noAF

Benign

-0.78

CADD

Benign

7.8

(source)

DANN

Benign

0.84

DEOGEN2

Benign

0.012

Eigen

Benign

-1.1

Eigen_PC

Benign

-0.86

FATHMM_MKL

Benign

0.013

LIST_S2

Benign

0.022

MetaRNN

Benign

0.0000011

MetaSVM

Benign

-0.98

MutationAssessor

Benign

-2.0

PhyloP100

-0.089

PrimateAI

Benign

0.45

PROVEAN

Benign

0.10

REVEL

Benign

0.047

Sift

Benign

0.95

Sift4G

Benign

0.82

Polyphen

0.0

Vest4

0.029

MPC

0.11

ClinPred

0.0042

GERP RS

2.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.019

gMVP

0.43

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over