chr10-20319985-C-T

Variant names:

• chr10-20319985-C-T
• rs10828015

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 0.39 in 151,946 control chromosomes in the GnomAD database, including 13,601 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 (13601 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.524 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: 0.390 AC: 59260 AN: 151828 Hom.: 13603 Cov.: 33

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.0834

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.390 AC: 59253 AN: 151946 Hom.: 13601 Cov.: 33 AF XY: 0.385 AC XY: 28560 AN XY: 74230

African (AFR) AF: 0.184 AC: 7614 AN: 41478

American (AMR) AF: 0.349 AC: 5320 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1807 AN: 3470

East Asian (EAS) AF: 0.0836 AC: 431 AN: 5158

South Asian (SAS) AF: 0.444 AC: 2138 AN: 4812

European-Finnish (FIN) AF: 0.435 AC: 4575 AN: 10528

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35888 AN: 67922

Other (OTH) AF: 0.421 AC: 888 AN: 2110

Alfa AF: 0.491 Hom.: 31359

Bravo AF: 0.369

Asia WGS AF: 0.237 AC: 826 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.81
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs10828015; hg19: chr10-20608914;