22-37042611-G-T

Position:

• chr22-37042611-G-T

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 0.474 in 150,774 control chromosomes in the GnomAD database, including 19,749 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 0.47 (19749 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.849

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.643 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: 0.474 AC: 71407 AN: 150678 Hom.: 19736 Cov.: 31

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.610

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.474 AC: 71438 AN: 150774 Hom.: 19749 Cov.: 31 AF XY: 0.481 AC XY: 35356 AN XY: 73580

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.526

Alfa AF: 0.559 Hom.: 12979

Bravo AF: 0.466

Asia WGS AF: 0.610 AC: 2121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.2
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs130624; hg19: chr22-37438651;