chr22-36878401-G-C

Position:

• chr22-36878401-G-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 0.12 in 152,142 control chromosomes in the GnomAD database, including 1,461 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 0.12 (1461 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 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: 0.120 AC: 18229 AN: 152024 Hom.: 1457 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0923

Gnomad EAS AF: 0.0544

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0574

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0683

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.120 AC: 18266 AN: 152142 Hom.: 1461 Cov.: 32 AF XY: 0.120 AC XY: 8907 AN XY: 74366

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.0923

Gnomad4 EAS AF: 0.0540

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0574

Gnomad4 NFE AF: 0.0683

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0230 Hom.: 11

Bravo AF: 0.132

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.0
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8137456; hg19: chr22-37274443;