rs10511885

Variant names:

• chr9-31831045-A-G
• rs10511885

Your query was ambiguous. Multiple possible variants found:

• chr9-31831045-A-G
• chr9-31831045-A-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 0.486 in 151,792 control chromosomes in the GnomAD database, including 18,858 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 0.49 (18858 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 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: 0.486 AC: 73687 AN: 151674 Hom.: 18847 Cov.: 31

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.486 AC: 73733 AN: 151792 Hom.: 18858 Cov.: 31 AF XY: 0.490 AC XY: 36348 AN XY: 74162

African (AFR) AF: 0.316 AC: 13092 AN: 41432

American (AMR) AF: 0.490 AC: 7460 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1861 AN: 3468

East Asian (EAS) AF: 0.549 AC: 2823 AN: 5144

South Asian (SAS) AF: 0.587 AC: 2822 AN: 4810

European-Finnish (FIN) AF: 0.573 AC: 6050 AN: 10562

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.556 AC: 37691 AN: 67832

Other (OTH) AF: 0.503 AC: 1060 AN: 2108

Alfa AF: 0.540 Hom.: 13182

Bravo AF: 0.467

Asia WGS AF: 0.577 AC: 2003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.7
DANN	Benign	0.55
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs10511885; hg19: chr9-31831043; COSMIC: COSV60351314;