4-144529807-A-G

Variant names:

• chr4-144529807-A-G
• rs1512285
• ENST00000649263.1:n.328-113829T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000649263.1(ENSG00000285713):​n.328-113829T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 151,928 control chromosomes in the GnomAD database, including 33,227 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 0.65 (33227 hom., cov: 31)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.94
• Publications: 8 publications found

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.823 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.328-113829T>C		intron	N/A	ENSP00000497507.1	A0A3B3ISY7
	ENSG00000285783	ENST00000650526.1		n.223-113829T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98723 AN: 151810 Hom.: 33190 Cov.: 31

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.650 AC: 98821 AN: 151928 Hom.: 33227 Cov.: 31 AF XY: 0.655 AC XY: 48662 AN XY: 74250

African (AFR) AF: 0.813 AC: 33686 AN: 41458

American (AMR) AF: 0.641 AC: 9773 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1806 AN: 3472

East Asian (EAS) AF: 0.618 AC: 3191 AN: 5164

South Asian (SAS) AF: 0.845 AC: 4071 AN: 4818

European-Finnish (FIN) AF: 0.617 AC: 6493 AN: 10520

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37882 AN: 67934

Other (OTH) AF: 0.604 AC: 1270 AN: 2104

Alfa AF: 0.609 Hom.: 15675

Bravo AF: 0.648

Asia WGS AF: 0.768 AC: 2671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	21
DANN	Benign	0.79
PhyloP100		2.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1512285;

hg19: chr4-145450959;