rs2025267

Variant names:

• chr6-4158288-G-A
• rs2025267
• ENST00000716024.1:n.440-865G>A

Variant summary

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

The ENST00000716024.1(ECI2-DT):​n.440-865G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.814 in 152,190 control chromosomes in the GnomAD database, including 50,984 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 0.81 (50984 hom., cov: 32)
• Consequence: ECI2-DT ENST00000716024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.712
• Publications: 4 publications found

Genes affected

ECI2-DT (HGNC:54425): (ECI2 divergent transcript)

LOC124901246 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901246	XR_007059416.1	n.999+12619G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ECI2-DT	ENST00000716024.1	n.440-865G>A		intron_variant	Intron 2 of 2
ECI2-DT	ENST00000716042.1	n.127-12867G>A		intron_variant	Intron 1 of 3
ECI2-DT	ENST00000808374.1	n.465-12867G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.814 AC: 123864 AN: 152074 Hom.: 50955 Cov.: 32

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.818

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.814 AC: 123951 AN: 152190 Hom.: 50984 Cov.: 32 AF XY: 0.817 AC XY: 60806 AN XY: 74390

African (AFR) AF: 0.924 AC: 38394 AN: 41536

American (AMR) AF: 0.793 AC: 12128 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2711 AN: 3468

East Asian (EAS) AF: 0.872 AC: 4509 AN: 5170

South Asian (SAS) AF: 0.857 AC: 4130 AN: 4818

European-Finnish (FIN) AF: 0.782 AC: 8268 AN: 10574

Middle Eastern (MID) AF: 0.812 AC: 237 AN: 292

European-Non Finnish (NFE) AF: 0.753 AC: 51200 AN: 68010

Other (OTH) AF: 0.808 AC: 1705 AN: 2110

Alfa AF: 0.776 Hom.: 85344

Bravo AF: 0.817

Asia WGS AF: 0.876 AC: 3049 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	0.037
DANN	Benign	0.72
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs2025267; hg19: chr6-4158522;