4-176871147-C-T

Variant names:

• chr4-176871147-C-T
• rs2333575
• ENST00000510203.1:n.128+4029G>A

Variant summary

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

The ENST00000510203.1(ENSG00000249458):​n.128+4029G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 151,934 control chromosomes in the GnomAD database, including 25,637 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 0.53 (25637 hom., cov: 31)
• Consequence: ENSG00000249458 ENST00000510203.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668

Genes affected

ENSG00000249458 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.685 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
ENSG00000249458	ENST00000510203.1	n.128+4029G>A		intron_variant	Intron 2 of 2	3
ENSG00000287544	ENST00000656694.1	n.384+22721G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79826 AN: 151816 Hom.: 25634 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.525 AC: 79829 AN: 151934 Hom.: 25637 Cov.: 31 AF XY: 0.528 AC XY: 39171 AN XY: 74252

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.573

Alfa AF: 0.465 Hom.: 1622

Bravo AF: 0.504

Asia WGS AF: 0.545 AC: 1897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.73
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2333575; hg19: chr4-177792301;