rs9332101

Positions:

• chr10-94938198-T-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The variant allele was found at a frequency of 0.0878 in 152,256 control chromosomes in the GnomAD database, including 741 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.088 (741 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.71

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BP6: Variant 10-94938198-T-A is Benign according to our data. Variant chr10-94938198-T-A is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0879 AC: 13373 AN: 152138 Hom.: 741 Cov.: 32

Gnomad AFR AF: 0.0234

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.0979

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0393

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0878 AC: 13368 AN: 152256 Hom.: 741 Cov.: 32 AF XY: 0.0866 AC XY: 6447 AN XY: 74434

Gnomad4 AFR AF: 0.0234

Gnomad4 AMR AF: 0.0978

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0393

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0995 Hom.: 106

Bravo AF: 0.0858

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.24
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332101; hg19: chr10-96697955;