Genetic Variant SLC17A1:p.Val201Ile (chr6-25819083-C-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_005074.5(SLC17A1):c.601G>A(p.Val201Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SLC17A1
NM_005074.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.05

Publications

0 publications found

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 was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.19027647).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC17A1	NM_005074.5 link	c.601G>A	p.Val201Ile	missense_variant	Exon 6 of 13	ENST00000244527.10	NP_005065.2	Q14916-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLC17A1	ENST00000244527.10 link	c.601G>A	p.Val201Ile	missense_variant	Exon 6 of 13	5	NM_005074.5	ENSP00000244527.4	Q14916-1
SLC17A1	ENST00000468082.1 link	c.601G>A	p.Val201Ile	missense_variant	Exon 5 of 10	1		ENSP00000420546.1	Q14916-2
SLC17A1	ENST00000476801.5 link	c.601G>A	p.Val201Ile	missense_variant	Exon 6 of 12	2		ENSP00000420614.1	Q14916-1
SLC17A1	ENST00000377886.6 link	n.601G>A		non_coding_transcript_exon_variant	Exon 6 of 12	5		ENSP00000367118.2	E9PGW3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1450560

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

721322

African (AFR)

AF:

0.00

AC:

AN:

32768

American (AMR)

AF:

0.00

AC:

AN:

42116

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25756

East Asian (EAS)

AF:

0.00

AC:

AN:

39432

South Asian (SAS)

AF:

0.00

AC:

AN:

83246

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53166

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5702

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1108552

Other (OTH)

AF:

0.00

AC:

AN:

59822

GnomAD4 genome

Cov.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Apr 04, 2023

Ambry Genetics

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

The c.601G>A (p.V201I) alteration is located in exon 6 (coding exon 5) of the SLC17A1 gene. This alteration results from a G to A substitution at nucleotide position 601, causing the valine (V) at amino acid position 201 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.15

BayesDel_addAF

Benign

-0.16

BayesDel_noAF

Benign

-0.47

CADD

Benign

(source)

DANN

Benign

0.94

DEOGEN2

Benign

0.067

T;T;.

Eigen

Benign

-0.18

Eigen_PC

Benign

-0.054

FATHMM_MKL

Benign

0.55

LIST_S2

Benign

0.32

.;T;T

M_CAP

Benign

0.0078

MetaRNN

Benign

0.19

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.7

L;L;L

PhyloP100

1.1

PrimateAI

Benign

0.35

PROVEAN

Benign

-0.48

N;N;N

REVEL

Benign

0.047

Sift

Benign

0.52

T;T;T

Sift4G

Benign

0.39

T;T;T

Polyphen

0.072

B;B;B

Vest4

0.15

MutPred

0.39

Loss of catalytic residue at V201 (P = 0.0852);Loss of catalytic residue at V201 (P = 0.0852);Loss of catalytic residue at V201 (P = 0.0852);

MVP

0.62

MPC

0.42

ClinPred

0.81

GERP RS

3.5

Varity_R

0.071

gMVP

0.31

Mutation Taster

=92/8

polymorphism

(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

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over