chr22-37675036-G-A

Variant names:

• chr22-37675036-G-A
• rs4820294

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 0.3 in 152,090 control chromosomes in the GnomAD database, including 7,085 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 0.30 (7085 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38
• Publications: 36 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 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: 0.300 AC: 45620 AN: 151972 Hom.: 7093 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.300 AC: 45611 AN: 152090 Hom.: 7085 Cov.: 32 AF XY: 0.299 AC XY: 22195 AN XY: 74332

African (AFR) AF: 0.221 AC: 9188 AN: 41516

American (AMR) AF: 0.301 AC: 4605 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1561 AN: 3472

East Asian (EAS) AF: 0.259 AC: 1330 AN: 5130

South Asian (SAS) AF: 0.273 AC: 1319 AN: 4830

European-Finnish (FIN) AF: 0.317 AC: 3348 AN: 10570

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23191 AN: 67962

Other (OTH) AF: 0.317 AC: 671 AN: 2116

Alfa AF: 0.341 Hom.: 16648

Bravo AF: 0.295

Asia WGS AF: 0.285 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	16
DANN	Benign	0.85
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs4820294; hg19: chr22-38071043; COSMIC: COSV53222379;