chr22-36168122-G-A

Position:

• chr22-36168122-G-A

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 0.897 in 152,248 control chromosomes in the GnomAD database, including 61,562 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 0.90 (61562 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.965 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: 0.897 AC: 136506 AN: 152130 Hom.: 61502 Cov.: 30

Gnomad AFR AF: 0.973

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.913

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.897 AC: 136625 AN: 152248 Hom.: 61562 Cov.: 30 AF XY: 0.900 AC XY: 66995 AN XY: 74434

Gnomad4 AFR AF: 0.973

Gnomad4 AMR AF: 0.914

Gnomad4 ASJ AF: 0.887

Gnomad4 EAS AF: 0.953

Gnomad4 SAS AF: 0.904

Gnomad4 FIN AF: 0.911

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.889

Alfa AF: 0.873 Hom.: 12894

Bravo AF: 0.900

Asia WGS AF: 0.941 AC: 3271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs132665; hg19: chr22-36564170;