rs739240

Variant names:

• chr22-49658959-C-A
• rs739240

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 0.702 in 152,010 control chromosomes in the GnomAD database, including 37,852 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 0.70 (37852 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.775 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: 0.702 AC: 106626 AN: 151892 Hom.: 37819 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.702 AC: 106712 AN: 152010 Hom.: 37852 Cov.: 32 AF XY: 0.698 AC XY: 51818 AN XY: 74282

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.787

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.710

Alfa AF: 0.718 Hom.: 6443

Bravo AF: 0.712

Asia WGS AF: 0.528 AC: 1839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.84
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs739240; hg19: chr22-50052607;