4-144503691-G-A

Variant names:

• chr4-144503691-G-A
• rs12641251
• ENST00000649263.1:n.328-87713C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649263.1(ENSG00000285713):​n.328-87713C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 151,938 control chromosomes in the GnomAD database, including 27,306 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 0.58 (27306 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 2 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.681 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285713	ENST00000649263.1		n.328-87713C>T		intron	N/A	ENSP00000497507.1
	ENSG00000285783	ENST00000648340.1		n.138+5550C>T		intron	N/A
	ENSG00000285783	ENST00000650526.1		n.223-87713C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88184 AN: 151820 Hom.: 27282 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.581 AC: 88244 AN: 151938 Hom.: 27306 Cov.: 32 AF XY: 0.583 AC XY: 43303 AN XY: 74248

African (AFR) AF: 0.352 AC: 14575 AN: 41402

American (AMR) AF: 0.563 AC: 8585 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2141 AN: 3468

East Asian (EAS) AF: 0.668 AC: 3449 AN: 5160

South Asian (SAS) AF: 0.662 AC: 3186 AN: 4810

European-Finnish (FIN) AF: 0.716 AC: 7550 AN: 10552

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.687 AC: 46673 AN: 67976

Other (OTH) AF: 0.592 AC: 1247 AN: 2108

Alfa AF: 0.647 Hom.: 52099

Bravo AF: 0.557

Asia WGS AF: 0.569 AC: 1979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.062
DANN	Benign	0.50
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs12641251; hg19: chr4-145424843;