rs10981955

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 91 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.00868

Gnomad4 AMR AF: 0.0243

Gnomad4 ASJ AF: 0.0107

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0133

Gnomad4 FIN AF: 0.0396

Gnomad4 NFE AF: 0.0456

Gnomad4 OTH AF: 0.0265

Alfa AF: 0.0395 Hom.: 178

Bravo AF: 0.0273

Asia WGS AF: 0.00897 AC: 32 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10981955; hg19: chr9-116591472;