22-37675036-G-A

Position:

• chr22-37675036-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.317

Alfa AF: 0.344 Hom.: 12477

Bravo AF: 0.295

Asia WGS AF: 0.285 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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