ENST00000752489.1:n.282+13933T>G

Variant names:

• chr4-176534347-T-G
• rs309773
• ENST00000752489.1:n.282+13933T>G

Variant summary

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

The ENST00000752489.1(ENSG00000298014):​n.282+13933T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 150,336 control chromosomes in the GnomAD database, including 23,008 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 0.55 (23008 hom., cov: 31)
• Consequence: ENSG00000298014 ENST00000752489.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 3 publications found

Genes affected

ENSG00000298014 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752489.1. 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
	ENSG00000298014	ENST00000752489.1		n.282+13933T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.551 AC: 82848 AN: 150226 Hom.: 22984 Cov.: 31

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.551 AC: 82905 AN: 150336 Hom.: 23008 Cov.: 31 AF XY: 0.549 AC XY: 40253 AN XY: 73384

African (AFR) AF: 0.654 AC: 27022 AN: 41320

American (AMR) AF: 0.555 AC: 8318 AN: 14994

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1510 AN: 3422

East Asian (EAS) AF: 0.434 AC: 2229 AN: 5138

South Asian (SAS) AF: 0.611 AC: 2916 AN: 4776

European-Finnish (FIN) AF: 0.475 AC: 4893 AN: 10300

Middle Eastern (MID) AF: 0.528 AC: 151 AN: 286

European-Non Finnish (NFE) AF: 0.512 AC: 34376 AN: 67126

Other (OTH) AF: 0.566 AC: 1179 AN: 2082

Alfa AF: 0.548 Hom.: 3958

Bravo AF: 0.552

Asia WGS AF: 0.543 AC: 1886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.4
DANN	Benign	0.82
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs309773; hg19: chr4-177455498;