rs137636

Variant names:

• chr22-39326472-C-A
• rs137636

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.429

Alfa AF: 0.464 Hom.: 9232

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs137636; hg19: chr22-39722477;