rs739240

Positions:

• chr22-49658959-C-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 0.702 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.49658959C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;