10-93164567-A-T

Variant names:

• chr10-93164567-A-T
• rs10882165

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.386 in 151,900 control chromosomes in the GnomAD database, including 11,896 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 0.39 (11896 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.42 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: 0.387 AC: 58672 AN: 151780 Hom.: 11900 Cov.: 31

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.0187

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.435

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.386 AC: 58683 AN: 151900 Hom.: 11896 Cov.: 31 AF XY: 0.379 AC XY: 28163 AN XY: 74244

African (AFR) AF: 0.400 AC: 16565 AN: 41402

American (AMR) AF: 0.366 AC: 5585 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1346 AN: 3468

East Asian (EAS) AF: 0.0186 AC: 96 AN: 5168

South Asian (SAS) AF: 0.304 AC: 1463 AN: 4816

European-Finnish (FIN) AF: 0.342 AC: 3617 AN: 10572

Middle Eastern (MID) AF: 0.438 AC: 127 AN: 290

European-Non Finnish (NFE) AF: 0.424 AC: 28824 AN: 67910

Other (OTH) AF: 0.391 AC: 821 AN: 2102

Alfa AF: 0.419 Hom.: 1712

Bravo AF: 0.384

Asia WGS AF: 0.169 AC: 587 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.39
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs10882165; hg19: chr10-94924324;