Variant rs1165196 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005074.5(SLC17A1):c.806C>T(p.Thr269Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 1,612,780 control chromosomes in the GnomAD database, including 285,985 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.66 ( 35073 hom., cov: 32)

Exomes 𝑓: 0.58 ( 250912 hom. )

Consequence

SLC17A1
NM_005074.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.96

Variant links:

Genes affected

SLC17A1 (HGNC:10929): (solute carrier family 17 member 1) Predicted to enable sialic acid transmembrane transporter activity. Involved in urate metabolic process and urate transport. Located in apical plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC17A1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.819695E-6).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC17A1	NM_005074.5 linkuse as main transcript	c.806C>T	p.Thr269Ile	missense_variant	8/13	ENST00000244527.10	NP_005065.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC17A1	ENST00000244527.10 linkuse as main transcript	c.806C>T	p.Thr269Ile	missense_variant	8/13	5	NM_005074.5	ENSP00000244527	P1	Q14916-1
SLC17A1	ENST00000468082.1 linkuse as main transcript	c.735+173C>T		intron_variant		1		ENSP00000420546		Q14916-2
SLC17A1	ENST00000476801.5 linkuse as main transcript	c.806C>T	p.Thr269Ile	missense_variant	8/12	2		ENSP00000420614	P1	Q14916-1
SLC17A1	ENST00000377886.6 linkuse as main transcript	c.*57C>T		3_prime_UTR_variant, NMD_transcript_variant	7/12	5		ENSP00000367118

Frequencies

GnomAD3 genomes

AF:

0.661

AC:

100595

AN:

152074

Hom.:

35012

Cov.:

show subpopulations

Gnomad AFR

AF:

0.873

Gnomad AMI

AF:

0.342

Gnomad AMR

AF:

0.654

Gnomad ASJ

AF:

0.459

Gnomad EAS

AF:

0.832

Gnomad SAS

AF:

0.530

Gnomad FIN

AF:

0.643

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.548

Gnomad OTH

AF:

0.660

GnomAD3 exomes

AF:

0.618

AC:

155166

AN:

251110

Hom.:

50040

AF XY:

0.601

AC XY:

81630

AN XY:

135722

show subpopulations

Gnomad AFR exome

AF:

0.879

Gnomad AMR exome

AF:

0.725

Gnomad ASJ exome

AF:

0.470

Gnomad EAS exome

AF:

0.863

Gnomad SAS exome

AF:

0.527

Gnomad FIN exome

AF:

0.628

Gnomad NFE exome

AF:

0.546

Gnomad OTH exome

AF:

0.580

GnomAD4 exome

AF:

0.581

AC:

847989

AN:

1460588

Hom.:

250912

Cov.:

AF XY:

0.576

AC XY:

418689

AN XY:

726668

show subpopulations

Gnomad4 AFR exome

AF:

0.890

Gnomad4 AMR exome

AF:

0.713

Gnomad4 ASJ exome

AF:

0.481

Gnomad4 EAS exome

AF:

0.846

Gnomad4 SAS exome

AF:

0.529

Gnomad4 FIN exome

AF:

0.626

Gnomad4 NFE exome

AF:

0.560

Gnomad4 OTH exome

AF:

0.596

GnomAD4 genome

AF:

0.662

AC:

100717

AN:

152192

Hom.:

35073

Cov.:

AF XY:

0.663

AC XY:

49351

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.873

Gnomad4 AMR

AF:

0.655

Gnomad4 ASJ

AF:

0.459

Gnomad4 EAS

AF:

0.832

Gnomad4 SAS

AF:

0.530

Gnomad4 FIN

AF:

0.643

Gnomad4 NFE

AF:

0.548

Gnomad4 OTH

AF:

0.661

Alfa

AF:

0.568

Hom.:

63233

Bravo

AF:

0.678

TwinsUK

AF:

0.558

AC:

2070

ALSPAC

AF:

0.555

AC:

2138

ESP6500AA

AF:

0.861

AC:

3795

ESP6500EA

AF:

0.546

AC:

4698

ExAC

AF:

0.616

AC:

74777

Asia WGS

AF:

0.681

AC:

2369

AN:

3478

EpiCase

AF:

0.541

EpiControl

AF:

0.532

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.067

BayesDel_addAF

Benign

-0.75

BayesDel_noAF

Benign

-0.70

CADD

Benign

6.5

DANN

Benign

0.32

DEOGEN2

Benign

0.050

T;T

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.000080

LIST_S2

Benign

0.14

.;T

MetaRNN

Benign

0.0000018

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.94

N;N

MutationTaster

Benign

1.0

P;P;P;P

PrimateAI

Benign

0.33

PROVEAN

Benign

2.9

N;N

REVEL

Benign

0.11

Sift

Benign

0.37

T;T

Sift4G

Benign

0.48

T;T

Polyphen

0.0

B;B

Vest4

0.029

MPC

0.10

ClinPred

0.0078

GERP RS

3.7

Varity_R

0.031

gMVP

0.071

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

LitVar

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over