4-116214224-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000508414.5(ENSG00000249259):​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: ENSG00000249259 ENST00000508414.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648

Genes affected

ENSG00000249259 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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
ENSG00000249259	ENST00000508414.5	n.203-17487G>A		intron_variant	Intron 1 of 2	3
ENSG00000249259	ENST00000509983.1	n.200-17487G>A		intron_variant	Intron 1 of 2	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

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.780

Gnomad4 ASJ AF: 0.818

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.862

Gnomad4 FIN AF: 0.932

Gnomad4 NFE AF: 0.873

Gnomad4 OTH AF: 0.700

Alfa AF: 0.843 Hom.: 71839

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1525760; hg19: chr4-117135380;