rs739240

Variant names:

• chr22-49658959-C-A
• rs739240

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.705 AC: 29227 AN: 41458

American (AMR) AF: 0.787 AC: 12028 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2500 AN: 3472

East Asian (EAS) AF: 0.472 AC: 2428 AN: 5148

South Asian (SAS) AF: 0.611 AC: 2946 AN: 4818

European-Finnish (FIN) AF: 0.666 AC: 7023 AN: 10546

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48485 AN: 67974

Other (OTH) AF: 0.710 AC: 1495 AN: 2106

Alfa AF: 0.718 Hom.: 6640

Bravo AF: 0.712

Asia WGS AF: 0.528 AC: 1839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.84
DANN	Benign	0.35
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs739240; hg19: chr22-50052607;