rs9332098

Positions:

• chr10-94937702-G-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 0.0496 in 152,260 control chromosomes in the GnomAD database, including 246 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 0.050 (246 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 10-94937702-G-A is Benign according to our data. Variant chr10-94937702-G-A is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.94937702G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0497 AC: 7561 AN: 152142 Hom.: 247 Cov.: 32

Gnomad AFR AF: 0.0131

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.0494

Gnomad ASJ AF: 0.0827

Gnomad EAS AF: 0.0312

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0562

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0662

Gnomad OTH AF: 0.0537

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

GnomAD4 genome AF: 0.0496 AC: 7555 AN: 152260 Hom.: 246 Cov.: 32 AF XY: 0.0503 AC XY: 3741 AN XY: 74440

Gnomad4 AFR AF: 0.0131

Gnomad4 AMR AF: 0.0492

Gnomad4 ASJ AF: 0.0827

Gnomad4 EAS AF: 0.0313

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0562

Gnomad4 NFE AF: 0.0662

Gnomad4 OTH AF: 0.0522

Alfa AF: 0.0596 Hom.: 114

Bravo AF: 0.0465

Asia WGS AF: 0.0770 AC: 267 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	1.7
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332098; hg19: chr10-96697459;