ENST00000725824.1:n.217+18231A>G

Variant names:

• chr11-6706237-A-G
• rs1395558
• ENST00000725824.1:n.217+18231A>G

Variant summary

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

The ENST00000725824.1(ENSG00000294763):​n.217+18231A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 152,070 control chromosomes in the GnomAD database, including 24,752 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 0.56 (24752 hom., cov: 32)
• Consequence: ENSG00000294763 ENST00000725824.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 6 publications found

Genes affected

ENSG00000294763 (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 (NFE) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000725824.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294763	ENST00000725824.1		n.217+18231A>G		intron	N/A
	ENSG00000294763	ENST00000725825.1		n.230+18231A>G		intron	N/A
	ENSG00000291143	ENST00000725921.1		n.117-5584T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84490 AN: 151952 Hom.: 24747 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.556 AC: 84519 AN: 152070 Hom.: 24752 Cov.: 32 AF XY: 0.554 AC XY: 41165 AN XY: 74304

African (AFR) AF: 0.362 AC: 15015 AN: 41456

American (AMR) AF: 0.523 AC: 7995 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2335 AN: 3470

East Asian (EAS) AF: 0.487 AC: 2522 AN: 5182

South Asian (SAS) AF: 0.486 AC: 2341 AN: 4820

European-Finnish (FIN) AF: 0.703 AC: 7438 AN: 10576

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44774 AN: 67974

Other (OTH) AF: 0.584 AC: 1232 AN: 2108

Alfa AF: 0.638 Hom.: 95704

Bravo AF: 0.533

Asia WGS AF: 0.467 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.13
DANN	Benign	0.37
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1395558; hg19: chr11-6727468;