4-144600715-A-G

Variant names:

• chr4-144600715-A-G
• rs2035901
• ENST00000649263.1:n.328-184737T>C

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-184737T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 151,980 control chromosomes in the GnomAD database, including 28,409 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 0.60 (28409 hom., cov: 31)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03
• Publications: 16 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=-1.14).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.782 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.328-184737T>C		intron	N/A	ENSP00000497507.1
	ENSG00000285783	ENST00000650526.1		n.222+154442T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90893 AN: 151862 Hom.: 28374 Cov.: 31

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.558

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.599 AC: 90988 AN: 151980 Hom.: 28409 Cov.: 31 AF XY: 0.606 AC XY: 44981 AN XY: 74280

African (AFR) AF: 0.751 AC: 31130 AN: 41464

American (AMR) AF: 0.584 AC: 8925 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1741 AN: 3470

East Asian (EAS) AF: 0.764 AC: 3944 AN: 5164

South Asian (SAS) AF: 0.803 AC: 3867 AN: 4814

European-Finnish (FIN) AF: 0.583 AC: 6144 AN: 10536

Middle Eastern (MID) AF: 0.549 AC: 158 AN: 288

European-Non Finnish (NFE) AF: 0.493 AC: 33474 AN: 67950

Other (OTH) AF: 0.565 AC: 1193 AN: 2112

Alfa AF: 0.513 Hom.: 11477

Bravo AF: 0.601

Asia WGS AF: 0.802 AC: 2790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.024
DANN	Benign	0.15
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs2035901; hg19: chr4-145521867;