10-8475697-C-T

Variant names:

• chr10-8475697-C-T
• rs7085991

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;