4-176871147-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000249458 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510203.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249458	ENST00000510203.1	TSL:3	n.128+4029G>A		intron	N/A
	ENSG00000287544	ENST00000656694.1		n.384+22721G>A		intron	N/A

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

African (AFR) AF: 0.131 AC: 5447 AN: 41448

American (AMR) AF: 0.631 AC: 9633 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2492 AN: 3464

East Asian (EAS) AF: 0.678 AC: 3499 AN: 5162

South Asian (SAS) AF: 0.532 AC: 2548 AN: 4792

European-Finnish (FIN) AF: 0.693 AC: 7313 AN: 10552

Middle Eastern (MID) AF: 0.634 AC: 185 AN: 292

European-Non Finnish (NFE) AF: 0.690 AC: 46864 AN: 67944

Other (OTH) AF: 0.573 AC: 1207 AN: 2106

Alfa AF: 0.442 Hom.: 1627

Bravo AF: 0.504

Asia WGS AF: 0.545 AC: 1897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.73
DANN	Benign	0.59
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs2333575; hg19: chr4-177792301;