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GeneBe

3-196217893-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_152672.6(SLC51A):c.90C>T(p.Ser30=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00448 in 1,613,508 control chromosomes in the GnomAD database, including 286 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.024 ( 157 hom., cov: 32)
Exomes 𝑓: 0.0024 ( 129 hom. )

Consequence

SLC51A
NM_152672.6 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.17
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]
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 3-196217893-C-T is Benign according to our data. Variant chr3-196217893-C-T is described in ClinVar as [Benign]. Clinvar id is 783411.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.17 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0815 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC51ANM_152672.6 linkuse as main transcriptc.90C>T p.Ser30= synonymous_variant 2/9 ENST00000296327.10
LOC105374304XR_001740544.2 linkuse as main transcriptn.1130+771G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC51AENST00000296327.10 linkuse as main transcriptc.90C>T p.Ser30= synonymous_variant 2/91 NM_152672.6 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0240
AC:
3656
AN:
152080
Hom.:
157
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0837
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00891
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0348
Gnomad NFE
AF:
0.000221
Gnomad OTH
AF:
0.0135
GnomAD3 exomes
AF:
0.00597
AC:
1490
AN:
249714
Hom.:
42
AF XY:
0.00443
AC XY:
598
AN XY:
135018
show subpopulations
Gnomad AFR exome
AF:
0.0824
Gnomad AMR exome
AF:
0.00334
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000329
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000284
Gnomad OTH exome
AF:
0.00313
GnomAD4 exome
AF:
0.00243
AC:
3552
AN:
1461310
Hom.:
129
Cov.:
31
AF XY:
0.00206
AC XY:
1496
AN XY:
726902
show subpopulations
Gnomad4 AFR exome
AF:
0.0859
Gnomad4 AMR exome
AF:
0.00403
Gnomad4 ASJ exome
AF:
0.0000766
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000128
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000162
Gnomad4 OTH exome
AF:
0.00472
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0241
AC:
3671
AN:
152198
Hom.:
157
Cov.:
32
AF XY:
0.0233
AC XY:
1733
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.0838
Gnomad4 AMR
AF:
0.00890
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000221
Gnomad4 OTH
AF:
0.0133
Alfa
AF:
0.0110
Hom.:
33
Bravo
AF:
0.0275
Asia WGS
AF:
0.00375
AC:
14
AN:
3478
EpiCase
AF:
0.000327
EpiControl
AF:
0.000594

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeMar 29, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
Cadd
Benign
10
Dann
Benign
0.54
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs34352044; hg19: chr3-195944764; API