rs391763

Variant names:

• chr5-163862989-G-A
• rs391763

Your query was ambiguous. Multiple possible variants found:

• chr5-163862989-G-A
• chr5-163862989-G-C
• chr5-163862989-G-T

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 0.654 in 151,270 control chromosomes in the GnomAD database, including 32,485 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 (32485 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 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: 0.654 AC: 98900 AN: 151154 Hom.: 32487 Cov.: 31

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.654 AC: 98928 AN: 151270 Hom.: 32485 Cov.: 31 AF XY: 0.649 AC XY: 47965 AN XY: 73850

African (AFR) AF: 0.644 AC: 26625 AN: 41326

American (AMR) AF: 0.701 AC: 10636 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2596 AN: 3466

East Asian (EAS) AF: 0.823 AC: 4213 AN: 5122

South Asian (SAS) AF: 0.587 AC: 2825 AN: 4812

European-Finnish (FIN) AF: 0.581 AC: 6069 AN: 10448

Middle Eastern (MID) AF: 0.723 AC: 211 AN: 292

European-Non Finnish (NFE) AF: 0.648 AC: 43790 AN: 67618

Other (OTH) AF: 0.671 AC: 1408 AN: 2098

Alfa AF: 0.638 Hom.: 3714

Bravo AF: 0.671

Asia WGS AF: 0.633 AC: 2198 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.36
DANN	Benign	0.23
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs391763; hg19: chr5-163289995;