rs942377

Variant names:

• chr6-25792064-T-C
• rs942377
• NM_005074.5:c.*2+6719A>G

Variant summary

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

The NM_005074.5(SLC17A1):​c.*2+6719A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,094 control chromosomes in the GnomAD database, including 6,388 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 0.28 (6388 hom., cov: 32)
• Consequence: SLC17A1 NM_005074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446
• Publications: 9 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC17A1	NM_005074.5	c.*2+6719A>G		intron_variant	Intron 12 of 12	ENST00000244527.10	NP_005065.2
SLC17A1	XM_017011201.3	c.*2+6719A>G		intron_variant	Intron 12 of 12		XP_016866690.2
SLC17A1	XM_011514818.3	c.1179-8846A>G		intron_variant	Intron 10 of 10		XP_011513120.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC17A1	ENST00000244527.10	c.*2+6719A>G		intron_variant	Intron 12 of 12	5	NM_005074.5	ENSP00000244527.4
SLC17A1	ENST00000377886.6	n.*657+6719A>G		intron_variant	Intron 11 of 11	5		ENSP00000367118.2

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42288 AN: 151976 Hom.: 6377 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.278 AC: 42307 AN: 152094 Hom.: 6388 Cov.: 32 AF XY: 0.274 AC XY: 20341 AN XY: 74348

African (AFR) AF: 0.399 AC: 16538 AN: 41454

American (AMR) AF: 0.215 AC: 3292 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 886 AN: 3472

East Asian (EAS) AF: 0.133 AC: 689 AN: 5174

South Asian (SAS) AF: 0.189 AC: 911 AN: 4820

European-Finnish (FIN) AF: 0.220 AC: 2334 AN: 10592

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16885 AN: 67980

Other (OTH) AF: 0.295 AC: 622 AN: 2110

Alfa AF: 0.270 Hom.: 897

Bravo AF: 0.286

Asia WGS AF: 0.162 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.69
PhyloP100		0.45
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: rs942377; hg19: chr6-25792292;