rs4924134

Variant names:

• chr15-34702364-A-G
• rs4924134
• ENST00000720751.1:n.234+17953T>C

Your query was ambiguous. Multiple possible variants found:

• chr15-34702364-A-G
• chr15-34702364-A-T

Variant summary

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

The ENST00000720751.1(ENSG00000294065):​n.234+17953T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,918 control chromosomes in the GnomAD database, including 12,791 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 0.41 (12791 hom., cov: 31)
• Consequence: ENSG00000294065 ENST00000720751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.877
• Publications: 7 publications found

Genes affected

ENSG00000294065 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720751.1. 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
	ENSG00000294065	ENST00000720751.1		n.234+17953T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61908 AN: 151800 Hom.: 12786 Cov.: 31

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.408 AC: 61946 AN: 151918 Hom.: 12791 Cov.: 31 AF XY: 0.406 AC XY: 30175 AN XY: 74248

African (AFR) AF: 0.377 AC: 15605 AN: 41402

American (AMR) AF: 0.372 AC: 5674 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1196 AN: 3468

East Asian (EAS) AF: 0.437 AC: 2263 AN: 5174

South Asian (SAS) AF: 0.587 AC: 2829 AN: 4816

European-Finnish (FIN) AF: 0.347 AC: 3667 AN: 10556

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.430 AC: 29174 AN: 67922

Other (OTH) AF: 0.406 AC: 858 AN: 2114

Alfa AF: 0.403 Hom.: 1617

Bravo AF: 0.404

Asia WGS AF: 0.517 AC: 1798 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.53
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs4924134; hg19: chr15-34994565;