22-38797061-C-T

Position:

• chr22-38797061-C-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 0.809 in 152,068 control chromosomes in the GnomAD database, including 49,968 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 0.81 (49968 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.809 AC: 122998 AN: 151950 Hom.: 49928 Cov.: 31

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.809 AC: 123091 AN: 152068 Hom.: 49968 Cov.: 31 AF XY: 0.810 AC XY: 60195 AN XY: 74336

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.780

Gnomad4 EAS AF: 0.892

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.815

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.802

Alfa AF: 0.822 Hom.: 23423

Bravo AF: 0.811

Asia WGS AF: 0.868 AC: 3017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.1
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs738141; hg19: chr22-39193066;