4-144787534-C-T

Position:

• chr4-144787534-C-T

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.327+277038G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 151,974 control chromosomes in the GnomAD database, including 44,768 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 0.75 (44768 hom., cov: 31)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.144787534C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.327+277038G>A		intron_variant				ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.94-32249G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114618 AN: 151854 Hom.: 44772 Cov.: 31

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.754 AC: 114643 AN: 151974 Hom.: 44768 Cov.: 31 AF XY: 0.752 AC XY: 55867 AN XY: 74294

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.732

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.876

Gnomad4 OTH AF: 0.783

Alfa AF: 0.837 Hom.: 27388

Bravo AF: 0.741

Asia WGS AF: 0.614 AC: 2137 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	14
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12647866; hg19: chr4-145708686;