5-13681650-G-A

Variant names:

• chr5-13681650-G-A
• rs2034222

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 0.511 in 151,872 control chromosomes in the GnomAD database, including 20,017 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 0.51 (20017 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 3 publications found

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 (NFE) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77477 AN: 151756 Hom.: 20003 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.511 AC: 77546 AN: 151872 Hom.: 20017 Cov.: 32 AF XY: 0.506 AC XY: 37547 AN XY: 74222

African (AFR) AF: 0.489 AC: 20246 AN: 41404

American (AMR) AF: 0.493 AC: 7515 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1931 AN: 3470

East Asian (EAS) AF: 0.394 AC: 2028 AN: 5142

South Asian (SAS) AF: 0.422 AC: 2029 AN: 4812

European-Finnish (FIN) AF: 0.536 AC: 5649 AN: 10544

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36379 AN: 67940

Other (OTH) AF: 0.518 AC: 1091 AN: 2106

Alfa AF: 0.512 Hom.: 2960

Bravo AF: 0.510

Asia WGS AF: 0.442 AC: 1539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.59
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs2034222; hg19: chr5-13681759;