22-36036289-A-T

Variant names:

• chr22-36036289-A-T
• rs739200

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 0.287 in 152,108 control chromosomes in the GnomAD database, including 11,577 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 0.29 (11577 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43551 AN: 151990 Hom.: 11531 Cov.: 31

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0822

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0973

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.287 AC: 43652 AN: 152108 Hom.: 11577 Cov.: 31 AF XY: 0.277 AC XY: 20595 AN XY: 74354

Gnomad4 AFR AF: 0.712

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.0824

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0973

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.225

Alfa AF: 0.0749 Hom.: 100

Bravo AF: 0.311

Asia WGS AF: 0.139 AC: 486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs739200; hg19: chr22-36432337;