4-144531631-C-T

Position:

• chr4-144531631-C-T

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-115653G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 152,034 control chromosomes in the GnomAD database, including 30,033 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 0.62 (30033 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377462	XR_939272.3	n.164+30353G>A		intron_variant
LOC105377462	XR_939273.3	n.164+30353G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.328-115653G>A		intron_variant				ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.223-115653G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94445 AN: 151916 Hom.: 30010 Cov.: 32

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.622 AC: 94526 AN: 152034 Hom.: 30033 Cov.: 32 AF XY: 0.627 AC XY: 46591 AN XY: 74294

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.818

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.581

Alfa AF: 0.576 Hom.: 34795

Bravo AF: 0.617

Asia WGS AF: 0.751 AC: 2613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.57
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6845536; hg19: chr4-145452783;