rs2865892

chr20-40775256-C-T

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 0.143 in 152,148 control chromosomes in the GnomAD database, including 1,675 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 0.14 (1675 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.277 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: 0.143 AC: 21772 AN: 152030 Hom.: 1671 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.143 AC: 21803 AN: 152148 Hom.: 1675 Cov.: 32 AF XY: 0.144 AC XY: 10735 AN XY: 74382

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.133

Alfa AF: 0.131 Hom.: 629

Bravo AF: 0.147

Asia WGS AF: 0.214 AC: 742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.34
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2865892; hg19: chr20-39403896;