chr22-39087962-T-C

Position:

• chr22-39087962-T-C

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 0.658 in 151,776 control chromosomes in the GnomAD database, including 32,977 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 0.66 (32977 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.88

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.39087962T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99763 AN: 151660 Hom.: 32962 Cov.: 31

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.658 AC: 99822 AN: 151776 Hom.: 32977 Cov.: 31 AF XY: 0.653 AC XY: 48406 AN XY: 74134

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.725

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.695

Alfa AF: 0.648 Hom.: 3736

Bravo AF: 0.675

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.65
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5757472; hg19: chr22-39483967;