rs137636

Variant names:

• chr22-39326472-C-A
• rs137636

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.404 in 151,562 control chromosomes in the GnomAD database, including 13,402 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 0.40 (13402 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 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: 0.404 AC: 61148 AN: 151446 Hom.: 13397 Cov.: 31

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.404 AC: 61162 AN: 151562 Hom.: 13402 Cov.: 31 AF XY: 0.398 AC XY: 29444 AN XY: 74042

African (AFR) AF: 0.262 AC: 10843 AN: 41344

American (AMR) AF: 0.450 AC: 6780 AN: 15076

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1977 AN: 3470

East Asian (EAS) AF: 0.129 AC: 660 AN: 5110

South Asian (SAS) AF: 0.368 AC: 1771 AN: 4806

European-Finnish (FIN) AF: 0.422 AC: 4446 AN: 10528

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.489 AC: 33189 AN: 67924

Other (OTH) AF: 0.429 AC: 901 AN: 2100

Alfa AF: 0.463 Hom.: 12387

Bravo AF: 0.399

Asia WGS AF: 0.233 AC: 809 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	1.4
DANN	Benign	0.91
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs137636; hg19: chr22-39722477;