ENST00000514290.1:n.117+40716G>A

Variant names:

• chr4-23601755-G-A
• rs4697041
• ENST00000514290.1:n.117+40716G>A

Variant summary

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

The ENST00000514290.1(ENSG00000250137):​n.117+40716G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,110 control chromosomes in the GnomAD database, including 14,171 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 0.43 (14171 hom., cov: 30)
• Consequence: ENSG00000250137 ENST00000514290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691
• Publications: 2 publications found

Genes affected

ENSG00000250137 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000514290.1. 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
	ENSG00000250137	ENST00000514290.1	TSL:4	n.117+40716G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.430 AC: 64855 AN: 151000 Hom.: 14142 Cov.: 30

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.430 AC: 64939 AN: 151110 Hom.: 14171 Cov.: 30 AF XY: 0.434 AC XY: 31964 AN XY: 73724

African (AFR) AF: 0.503 AC: 20707 AN: 41178

American (AMR) AF: 0.405 AC: 6141 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1128 AN: 3466

East Asian (EAS) AF: 0.499 AC: 2552 AN: 5112

South Asian (SAS) AF: 0.438 AC: 2099 AN: 4792

European-Finnish (FIN) AF: 0.427 AC: 4391 AN: 10288

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.392 AC: 26571 AN: 67804

Other (OTH) AF: 0.432 AC: 906 AN: 2098

Alfa AF: 0.393 Hom.: 12898

Bravo AF: 0.428

Asia WGS AF: 0.477 AC: 1663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.48
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs4697041; hg19: chr4-23603378;