6-25830070-A-G

Variant names:

• chr6-25830070-A-G
• rs1165176
• NM_005074.5:c.34+454T>C

Variant summary

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

The NM_005074.5(SLC17A1):​c.34+454T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 152,138 control chromosomes in the GnomAD database, including 34,185 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 0.65 (34185 hom., cov: 31)
• Consequence: SLC17A1 NM_005074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 13 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC17A1	NM_005074.5	c.34+454T>C		intron_variant	Intron 2 of 12	ENST00000244527.10	NP_005065.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC17A1	ENST00000244527.10	c.34+454T>C		intron_variant	Intron 2 of 12	5	NM_005074.5	ENSP00000244527.4
SLC17A1	ENST00000468082.1	c.34+454T>C		intron_variant	Intron 1 of 9	1		ENSP00000420546.1
SLC17A1	ENST00000476801.5	c.34+454T>C		intron_variant	Intron 2 of 11	2		ENSP00000420614.1
SLC17A1	ENST00000377886.6	n.34+454T>C		intron_variant	Intron 2 of 11	5		ENSP00000367118.2

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98999 AN: 152020 Hom.: 34121 Cov.: 31

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.652 AC: 99126 AN: 152138 Hom.: 34185 Cov.: 31 AF XY: 0.652 AC XY: 48507 AN XY: 74378

African (AFR) AF: 0.876 AC: 36365 AN: 41532

American (AMR) AF: 0.647 AC: 9889 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1569 AN: 3472

East Asian (EAS) AF: 0.830 AC: 4296 AN: 5174

South Asian (SAS) AF: 0.511 AC: 2465 AN: 4824

European-Finnish (FIN) AF: 0.619 AC: 6546 AN: 10568

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36165 AN: 67978

Other (OTH) AF: 0.650 AC: 1371 AN: 2110

Alfa AF: 0.561 Hom.: 42388

Bravo AF: 0.670

Asia WGS AF: 0.670 AC: 2332 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.26
DANN	Benign	0.39
PhyloP100		-1.7
PromoterAI		0.015	Neutral
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: rs1165176; hg19: chr6-25830298;