4-144787534-C-T

Variant names:

• chr4-144787534-C-T
• rs12647866
• ENST00000649263.1:n.327+277038G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649263.1. 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
	ENSG00000285713	ENST00000649263.1		n.327+277038G>A		intron	N/A	ENSP00000497507.1	A0A3B3ISY7
	ENSG00000285783	ENST00000650526.1		n.94-32249G>A		intron	N/A

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

African (AFR) AF: 0.566 AC: 23463 AN: 41430

American (AMR) AF: 0.732 AC: 11148 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2807 AN: 3472

East Asian (EAS) AF: 0.557 AC: 2866 AN: 5144

South Asian (SAS) AF: 0.716 AC: 3458 AN: 4828

European-Finnish (FIN) AF: 0.813 AC: 8609 AN: 10586

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.876 AC: 59539 AN: 67974

Other (OTH) AF: 0.783 AC: 1653 AN: 2110

Alfa AF: 0.835 Hom.: 38131

Bravo AF: 0.741

Asia WGS AF: 0.614 AC: 2137 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	14
DANN	Benign	0.73
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs12647866; hg19: chr4-145708686;