dbSNP rs1165215: SLC17A1:c.*2+79C>T (chr6-25798704-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005074.5(SLC17A1):c.*2+79C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 1,335,000 control chromosomes in the GnomAD database, including 240,346 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.66 ( 35040 hom., cov: 31)

Exomes 𝑓: 0.58 ( 205306 hom. )

Consequence

SLC17A1
NM_005074.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.48

Publications

12 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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new If you want to explore the variant's impact on the transcript NM_005074.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005074.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC17A1	NM_005074.5	MANE Select	c.*2+79C>T		intron	N/A	NP_005065.2	Q14916-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC17A1	ENST00000244527.10	TSL:5 MANE Select	c.*2+79C>T	intron	N/A	ENSP00000244527.4	Q14916-1
SLC17A1	ENST00000476801.5	TSL:2	c.*81C>T	3_prime_UTR	Exon 12 of 12	ENSP00000420614.1	Q14916-1
SLC17A1	ENST00000867421.1		c.*2+79C>T	intron	N/A	ENSP00000537480.1

Frequencies

GnomAD3 genomes

AF:

0.661

AC:

100503

AN:

151934

Hom.:

34979

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:

0.644

Gnomad MID

AF:

0.561

Gnomad NFE

AF:

0.548

Gnomad OTH

AF:

0.659

GnomAD4 exome

AF:

0.583

AC:

690092

AN:

1182946

Hom.:

205306

Cov.:

AF XY:

0.579

AC XY:

337343

AN XY:

582218

show subpopulations

African (AFR)

AF:

0.891

AC:

24590

AN:

27588

American (AMR)

AF:

0.710

AC:

24491

AN:

34482

Ashkenazi Jewish (ASJ)

AF:

0.479

AC:

9683

AN:

20202

East Asian (EAS)

AF:

0.846

AC:

30740

AN:

36350

South Asian (SAS)

AF:

0.528

AC:

27171

AN:

51448

European-Finnish (FIN)

AF:

0.629

AC:

27792

AN:

44160

Middle Eastern (MID)

AF:

0.582

AC:

2854

AN:

4904

European-Non Finnish (NFE)

AF:

0.561

AC:

513551

AN:

914906

Other (OTH)

AF:

0.597

AC:

29220

AN:

48906

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

13290

26580

39870

53160

66450

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15244

30488

45732

60976

76220

<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:

0.662

AC:

100625

AN:

152054

Hom.:

35040

Cov.:

AF XY:

0.663

AC XY:

49303

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.873

AC:

36237

AN:

41488

American (AMR)

AF:

0.655

AC:

9996

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.459

AC:

1594

AN:

3470

East Asian (EAS)

AF:

0.832

AC:

4301

AN:

5172

South Asian (SAS)

AF:

0.530

AC:

2557

AN:

4822

European-Finnish (FIN)

AF:

0.644

AC:

6792

AN:

10544

Middle Eastern (MID)

AF:

0.551

AC:

162

AN:

294

European-Non Finnish (NFE)

AF:

0.548

AC:

37285

AN:

67986

Other (OTH)

AF:

0.660

AC:

1392

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1560

3120

4680

6240

7800

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

788

1576

2364

3152

3940

<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:

0.604

Hom.:

23096

Bravo

AF:

0.678

Asia WGS

AF:

0.680

AC:

2368

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.034

(source)

DANN

Benign

0.46

PhyloP100

-1.5

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over