chr22-39326472-C-A

Position:

• chr22-39326472-C-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.404 in 151,562 control chromosomes in the GnomAD database, including 13,402 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 0.40 (13402 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 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: 0.404 AC: 61148 AN: 151446 Hom.: 13397 Cov.: 31

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.404 AC: 61162 AN: 151562 Hom.: 13402 Cov.: 31 AF XY: 0.398 AC XY: 29444 AN XY: 74042

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.429

Alfa AF: 0.464 Hom.: 9232

Bravo AF: 0.399

Asia WGS AF: 0.233 AC: 809 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	1.4
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs137636; hg19: chr22-39722477;