10-86585845-T-C

Variant names:

• chr10-86585845-T-C
• rs2691052

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;