chr6-25803676-G-A

Variant names:

• chr6-25803676-G-A
• rs1165208
• NM_005074.5:c.1179-2696C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005074.5(SLC17A1):​c.1179-2696C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 151,894 control chromosomes in the GnomAD database, including 11,972 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 0.38 (11972 hom., cov: 31)
• Consequence: SLC17A1 NM_005074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.650
• Publications: 3 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC17A1	NM_005074.5	c.1179-2696C>T		intron_variant	Intron 10 of 12	ENST00000244527.10	NP_005065.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC17A1	ENST00000244527.10	c.1179-2696C>T		intron_variant	Intron 10 of 12	5	NM_005074.5	ENSP00000244527.4
SLC17A1	ENST00000468082.1	c.1017-2696C>T		intron_variant	Intron 8 of 9	1		ENSP00000420546.1
SLC17A1	ENST00000476801.5	c.1179-2696C>T		intron_variant	Intron 10 of 11	2		ENSP00000420614.1
SLC17A1	ENST00000377886.6	n.*430-2696C>T		intron_variant	Intron 9 of 11	5		ENSP00000367118.2

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58048 AN: 151776 Hom.: 11934 Cov.: 31

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.359

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.383 AC: 58148 AN: 151894 Hom.: 11972 Cov.: 31 AF XY: 0.389 AC XY: 28891 AN XY: 74264

African (AFR) AF: 0.473 AC: 19594 AN: 41396

American (AMR) AF: 0.439 AC: 6702 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 706 AN: 3468

East Asian (EAS) AF: 0.698 AC: 3605 AN: 5166

South Asian (SAS) AF: 0.341 AC: 1638 AN: 4806

European-Finnish (FIN) AF: 0.422 AC: 4444 AN: 10528

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20366 AN: 67936

Other (OTH) AF: 0.364 AC: 769 AN: 2114

Alfa AF: 0.331 Hom.: 1345

Bravo AF: 0.392

Asia WGS AF: 0.514 AC: 1788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.0
DANN	Benign	0.76
PhyloP100		0.65
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1165208; hg19: chr6-25803904;