chr4-176871147-C-T

Position:

• chr4-176871147-C-T

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, non coding transcript 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: ENST00000510203.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000510203.1	n.128+4029G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000656694.1	n.384+22721G>A		intron_variant, non_coding_transcript_variant

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;