rs10785877

Variant names:

• chr9-134233655-G-A
• rs10785877

Your query was ambiguous. Multiple possible variants found:

• chr9-134233655-G-A
• chr9-134233655-G-T

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 0.643 in 152,120 control chromosomes in the GnomAD database, including 31,692 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 0.64 (31692 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.82
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.754 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: 0.643 AC: 97682 AN: 152002 Hom.: 31658 Cov.: 33

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.643 AC: 97772 AN: 152120 Hom.: 31692 Cov.: 33 AF XY: 0.646 AC XY: 48012 AN XY: 74360

African (AFR) AF: 0.684 AC: 28366 AN: 41496

American (AMR) AF: 0.668 AC: 10211 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2545 AN: 3470

East Asian (EAS) AF: 0.774 AC: 3998 AN: 5166

South Asian (SAS) AF: 0.699 AC: 3368 AN: 4820

European-Finnish (FIN) AF: 0.579 AC: 6121 AN: 10574

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40860 AN: 67994

Other (OTH) AF: 0.668 AC: 1410 AN: 2112

Alfa AF: 0.620 Hom.: 53896

Bravo AF: 0.650

Asia WGS AF: 0.740 AC: 2574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.090
DANN	Benign	0.49
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs10785877; hg19: chr9-137125501;