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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716024.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ECI2-DT	ENST00000716024.1		n.440-865G>A		intron	N/A
	ECI2-DT	ENST00000716042.1		n.127-12867G>A		intron	N/A
	ECI2-DT	ENST00000808374.1		n.465-12867G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2025267;

hg19: chr6-4158522;