10-8352117-A-G

Variant names:

• chr10-8352117-A-G
• rs10905349

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;