chr10-27639397-G-A

Variant names:

• chr10-27639397-G-A
• rs1168587

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 0.362 in 152,022 control chromosomes in the GnomAD database, including 10,891 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 0.36 (10891 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.431 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: 0.362 AC: 55028 AN: 151904 Hom.: 10883 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.362 AC: 55074 AN: 152022 Hom.: 10891 Cov.: 32 AF XY: 0.364 AC XY: 27061 AN XY: 74308

African (AFR) AF: 0.221 AC: 9151 AN: 41464

American (AMR) AF: 0.377 AC: 5760 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1512 AN: 3472

East Asian (EAS) AF: 0.132 AC: 683 AN: 5174

South Asian (SAS) AF: 0.358 AC: 1724 AN: 4814

European-Finnish (FIN) AF: 0.505 AC: 5340 AN: 10564

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29557 AN: 67952

Other (OTH) AF: 0.372 AC: 785 AN: 2110

Alfa AF: 0.412 Hom.: 22175

Bravo AF: 0.343

Asia WGS AF: 0.230 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.57
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs1168587; hg19: chr10-27928326;