rs316762

Variant names:

• chr5-41716291-A-G
• rs316762

Variant summary

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

The variant allele was found at a frequency of 0.368 in 152,104 control chromosomes in the GnomAD database, including 12,221 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 0.37 (12221 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.924
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55833 AN: 151984 Hom.: 12192 Cov.: 32

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.0350

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.368 AC: 55915 AN: 152104 Hom.: 12221 Cov.: 32 AF XY: 0.367 AC XY: 27302 AN XY: 74336

African (AFR) AF: 0.607 AC: 25174 AN: 41474

American (AMR) AF: 0.346 AC: 5292 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1156 AN: 3470

East Asian (EAS) AF: 0.0351 AC: 182 AN: 5182

South Asian (SAS) AF: 0.319 AC: 1541 AN: 4824

European-Finnish (FIN) AF: 0.285 AC: 3012 AN: 10560

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18216 AN: 67986

Other (OTH) AF: 0.375 AC: 791 AN: 2112

Alfa AF: 0.303 Hom.: 15132

Bravo AF: 0.379

Asia WGS AF: 0.203 AC: 706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.20
PhyloP100		-0.92

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs316762; hg19: chr5-41716393;