rs961831

Positions:

• chr9-22362105-T-G

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 0.102 in 152,194 control chromosomes in the GnomAD database, including 935 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 0.10 (935 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.680

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15492 AN: 152076 Hom.: 932 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.0759

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.0225

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0595

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0860

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.102 AC: 15510 AN: 152194 Hom.: 935 Cov.: 32 AF XY: 0.101 AC XY: 7501 AN XY: 74420

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.0758

Gnomad4 ASJ AF: 0.0493

Gnomad4 EAS AF: 0.0226

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.0595

Gnomad4 NFE AF: 0.0860

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0868 Hom.: 1091

Bravo AF: 0.103

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.7
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs961831; hg19: chr9-22362104;