ENST00000807542.1:n.839+24105G>A

Variant names:

• chr2-118281022-G-A
• rs1878526
• ENST00000807542.1:n.839+24105G>A

Variant summary

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

The ENST00000807542.1(ENSG00000304983):​n.839+24105G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,012 control chromosomes in the GnomAD database, including 4,742 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 0.24 (4742 hom., cov: 33)
• Consequence: ENSG00000304983 ENST00000807542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493
• Publications: 26 publications found

Genes affected

ENSG00000304983 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807542.1. 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
	ENSG00000304983	ENST00000807542.1		n.839+24105G>A		intron	N/A
	ENSG00000304983	ENST00000807543.1		n.535-3144G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36694 AN: 151896 Hom.: 4728 Cov.: 33

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.242 AC: 36736 AN: 152012 Hom.: 4742 Cov.: 33 AF XY: 0.239 AC XY: 17782 AN XY: 74290

African (AFR) AF: 0.324 AC: 13443 AN: 41432

American (AMR) AF: 0.190 AC: 2904 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 676 AN: 3470

East Asian (EAS) AF: 0.355 AC: 1828 AN: 5146

South Asian (SAS) AF: 0.257 AC: 1236 AN: 4812

European-Finnish (FIN) AF: 0.141 AC: 1493 AN: 10578

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14372 AN: 67974

Other (OTH) AF: 0.225 AC: 474 AN: 2110

Alfa AF: 0.220 Hom.: 14803

Bravo AF: 0.246

Asia WGS AF: 0.277 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.74
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs1878526; hg19: chr2-119038598; COSMIC: COSV50679589;