10-8352117-A-G

Position:

• chr10-8352117-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.756 in 151,996 control chromosomes in the GnomAD database, including 44,210 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 0.76 (44210 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.943

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

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: 0.756 AC: 114883 AN: 151878 Hom.: 44163 Cov.: 31

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.756 AC: 114983 AN: 151996 Hom.: 44210 Cov.: 31 AF XY: 0.758 AC XY: 56336 AN XY: 74282

Gnomad4 AFR AF: 0.661

Gnomad4 AMR AF: 0.793

Gnomad4 ASJ AF: 0.872

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.862

Gnomad4 FIN AF: 0.833

Gnomad4 NFE AF: 0.801

Gnomad4 OTH AF: 0.794

Alfa AF: 0.799 Hom.: 49456

Bravo AF: 0.749

Asia WGS AF: 0.699 AC: 2433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.4
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10905349; hg19: chr10-8394080;