ENST00000514290.1:n.118-53303G>A

Variant names:

• chr4-23715016-G-A
• rs7677217
• ENST00000514290.1:n.118-53303G>A

Variant summary

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

The ENST00000514290.1(ENSG00000250137):​n.118-53303G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 151,510 control chromosomes in the GnomAD database, including 13,432 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 0.40 (13432 hom., cov: 31)
• Consequence: ENSG00000250137 ENST00000514290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59
• 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=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250137	ENST00000514290.1	TSL:4	n.118-53303G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61044 AN: 151394 Hom.: 13434 Cov.: 31

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.403 AC: 61052 AN: 151510 Hom.: 13432 Cov.: 31 AF XY: 0.400 AC XY: 29574 AN XY: 73980

African (AFR) AF: 0.238 AC: 9824 AN: 41260

American (AMR) AF: 0.416 AC: 6323 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1791 AN: 3472

East Asian (EAS) AF: 0.216 AC: 1108 AN: 5126

South Asian (SAS) AF: 0.347 AC: 1668 AN: 4812

European-Finnish (FIN) AF: 0.475 AC: 4947 AN: 10410

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.499 AC: 33910 AN: 67920

Other (OTH) AF: 0.427 AC: 896 AN: 2098

Alfa AF: 0.448 Hom.: 2561

Bravo AF: 0.393

Asia WGS AF: 0.298 AC: 1039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	17
DANN	Benign	0.83
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs7677217; hg19: chr4-23716639;