9-126322653-G-C

Variant names:

• chr9-126322653-G-C
• rs10819146

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 0.619 in 152,078 control chromosomes in the GnomAD database, including 29,511 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 0.62 (29511 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94069 AN: 151960 Hom.: 29507 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.619 AC: 94098 AN: 152078 Hom.: 29511 Cov.: 32 AF XY: 0.624 AC XY: 46415 AN XY: 74354

African (AFR) AF: 0.672 AC: 27882 AN: 41472

American (AMR) AF: 0.525 AC: 8020 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1890 AN: 3470

East Asian (EAS) AF: 0.395 AC: 2044 AN: 5174

South Asian (SAS) AF: 0.680 AC: 3275 AN: 4818

European-Finnish (FIN) AF: 0.754 AC: 7974 AN: 10578

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.605 AC: 41096 AN: 67966

Other (OTH) AF: 0.563 AC: 1191 AN: 2114

Alfa AF: 0.626 Hom.: 3704

Bravo AF: 0.600

Asia WGS AF: 0.540 AC: 1883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.71
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs10819146; hg19: chr9-129084932; COSMIC: COSV63257318;