rs10981955

Variant names:

• chr9-113829192-G-A
• rs10981955

Your query was ambiguous. Multiple possible variants found:

• chr9-113829192-G-A
• chr9-113829192-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0291 in 152,062 control chromosomes in the GnomAD database, including 91 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 0.029 (91 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.671
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0291 (4431/152062) while in subpopulation NFE AF = 0.0456 (3101/67968). AF 95% confidence interval is 0.0443. There are 91 homozygotes in GnomAd4. There are 2093 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 91 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0292 AC: 4432 AN: 151944 Hom.: 91 Cov.: 32

Gnomad AFR AF: 0.00870

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.0243

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0133

Gnomad FIN AF: 0.0396

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0456

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0291 AC: 4431 AN: 152062 Hom.: 91 Cov.: 32 AF XY: 0.0282 AC XY: 2093 AN XY: 74334

African (AFR) AF: 0.00868 AC: 360 AN: 41490

American (AMR) AF: 0.0243 AC: 371 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0107 AC: 37 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.0133 AC: 64 AN: 4816

European-Finnish (FIN) AF: 0.0396 AC: 418 AN: 10546

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0456 AC: 3101 AN: 67968

Other (OTH) AF: 0.0265 AC: 56 AN: 2114

Alfa AF: 0.0395 Hom.: 217

Bravo AF: 0.0273

Asia WGS AF: 0.00897 AC: 32 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.59
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs10981955; hg19: chr9-116591472;