rs738809

chr22-24009046-G-Achr22-24009046-G-C

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 0.72 in 152,018 control chromosomes in the GnomAD database, including 39,662 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 0.72 (39662 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109421 AN: 151902 Hom.: 39627 Cov.: 30

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.720 AC: 109501 AN: 152018 Hom.: 39662 Cov.: 30 AF XY: 0.725 AC XY: 53864 AN XY: 74296

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.777

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.719

Gnomad4 OTH AF: 0.713

Alfa AF: 0.723 Hom.: 35528

Bravo AF: 0.717

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.4

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs738809; hg19: chr22-24405492;