ENST00000508414.5:n.203-17487G>A

Variant names:

• chr4-116214224-C-T
• rs1525760
• ENST00000508414.5:n.203-17487G>A

Variant summary

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

The ENST00000508414.5(ENSG00000293005):​n.203-17487G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,052 control chromosomes in the GnomAD database, including 42,462 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 0.69 (42462 hom., cov: 31)
• Consequence: ENSG00000293005 ENST00000508414.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648
• Publications: 9 publications found

Genes affected

ENSG00000293005 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293005	ENST00000508414.5	n.203-17487G>A		intron_variant	Intron 1 of 2	3
ENSG00000293005	ENST00000509983.2	n.265-17487G>A		intron_variant	Intron 1 of 2	3
ENSG00000293005	ENST00000775331.1	n.412-17487G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104743 AN: 151934 Hom.: 42462 Cov.: 31

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.689 AC: 104744 AN: 152052 Hom.: 42462 Cov.: 31 AF XY: 0.697 AC XY: 51806 AN XY: 74348

African (AFR) AF: 0.226 AC: 9376 AN: 41452

American (AMR) AF: 0.780 AC: 11903 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 2840 AN: 3470

East Asian (EAS) AF: 0.899 AC: 4625 AN: 5146

South Asian (SAS) AF: 0.862 AC: 4161 AN: 4826

European-Finnish (FIN) AF: 0.932 AC: 9888 AN: 10610

Middle Eastern (MID) AF: 0.716 AC: 209 AN: 292

European-Non Finnish (NFE) AF: 0.873 AC: 59373 AN: 67982

Other (OTH) AF: 0.700 AC: 1475 AN: 2106

Alfa AF: 0.820 Hom.: 87757

Bravo AF: 0.655

Asia WGS AF: 0.821 AC: 2855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.34
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs1525760; hg19: chr4-117135380;