rs9615812

Positions:

• chr22-48221836-G-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 0.0928 in 152,158 control chromosomes in the GnomAD database, including 726 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 0.093 (726 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 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: 0.0929 AC: 14123 AN: 152040 Hom.: 728 Cov.: 33

Gnomad AFR AF: 0.0965

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0544

Gnomad ASJ AF: 0.0615

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0247

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0895

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

GnomAD4 genome AF: 0.0928 AC: 14118 AN: 152158 Hom.: 726 Cov.: 33 AF XY: 0.0893 AC XY: 6642 AN XY: 74380

Gnomad4 AFR AF: 0.0963

Gnomad4 AMR AF: 0.0544

Gnomad4 ASJ AF: 0.0615

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0249

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.0881

Alfa AF: 0.0993 Hom.: 130

Bravo AF: 0.0873

Asia WGS AF: 0.0170 AC: 58 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.088
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9615812; hg19: chr22-48617648;