chr9-135137855-T-G

Variant names:

• chr9-135137855-T-G
• rs10776934

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 0.736 in 151,920 control chromosomes in the GnomAD database, including 41,473 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 0.74 (41473 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.814 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: 0.736 AC: 111728 AN: 151802 Hom.: 41425 Cov.: 31

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.736 AC: 111826 AN: 151920 Hom.: 41473 Cov.: 31 AF XY: 0.733 AC XY: 54399 AN XY: 74222

African (AFR) AF: 0.822 AC: 34065 AN: 41460

American (AMR) AF: 0.679 AC: 10369 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2594 AN: 3466

East Asian (EAS) AF: 0.530 AC: 2704 AN: 5102

South Asian (SAS) AF: 0.689 AC: 3303 AN: 4796

European-Finnish (FIN) AF: 0.713 AC: 7539 AN: 10572

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48908 AN: 67932

Other (OTH) AF: 0.717 AC: 1515 AN: 2112

Alfa AF: 0.692 Hom.: 8387

Bravo AF: 0.736

Asia WGS AF: 0.659 AC: 2295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.30
DANN	Benign	0.48
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs10776934; hg19: chr9-138029701;