rs2865892

Variant names:

• chr20-40775256-C-T
• rs2865892
• ENST00000758964.1:n.168+2806G>A

Variant summary

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

The ENST00000758964.1(ENSG00000229771):​n.168+2806G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000229771 ENST00000758964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837
• Publications: 4 publications found

Genes affected

ENSG00000229771 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.277 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
ENSG00000229771	ENST00000758964.1	n.168+2806G>A		intron_variant	Intron 2 of 5

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

African (AFR) AF: 0.145 AC: 6008 AN: 41502

American (AMR) AF: 0.180 AC: 2749 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 409 AN: 3470

East Asian (EAS) AF: 0.289 AC: 1497 AN: 5174

South Asian (SAS) AF: 0.193 AC: 929 AN: 4816

European-Finnish (FIN) AF: 0.135 AC: 1433 AN: 10584

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8391 AN: 67996

Other (OTH) AF: 0.133 AC: 280 AN: 2112

Alfa AF: 0.131 Hom.: 699

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
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs2865892; hg19: chr20-39403896;