chr10-86585845-T-C

Position:

• chr10-86585845-T-C

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 0.757 in 152,104 control chromosomes in the GnomAD database, including 43,741 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 (43741 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 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: 0.757 AC: 115020 AN: 151986 Hom.: 43685 Cov.: 32

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.757 AC: 115132 AN: 152104 Hom.: 43741 Cov.: 32 AF XY: 0.757 AC XY: 56274 AN XY: 74376

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.733

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.735

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.754

Alfa AF: 0.755 Hom.: 7585

Bravo AF: 0.759

Asia WGS AF: 0.756 AC: 2633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2691052; hg19: chr10-88345602;