10-8475697-C-T

Position:

• chr10-8475697-C-T

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 0.309 in 151,970 control chromosomes in the GnomAD database, including 7,849 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 0.31 (7849 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 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: 0.309 AC: 46895 AN: 151852 Hom.: 7838 Cov.: 31

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.309 AC: 46929 AN: 151970 Hom.: 7849 Cov.: 31 AF XY: 0.317 AC XY: 23519 AN XY: 74268

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.321

Alfa AF: 0.290 Hom.: 9964

Bravo AF: 0.320

Asia WGS AF: 0.529 AC: 1836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.1
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7085991; hg19: chr10-8517660;