rs1168587

chr10-27639397-G-A

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 0.362 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.372

Alfa AF: 0.418 Hom.: 17850

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1168587; hg19: chr10-27928326;