chr3-138911752-C-T

Variant names:

• chr3-138911752-C-T
• rs6439828
• ENST00000724516.1:n.169+4104G>A

Variant summary

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

The ENST00000724516.1(ENSG00000294582):​n.169+4104G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 152,098 control chromosomes in the GnomAD database, including 29,573 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 0.61 (29573 hom., cov: 33)
• Consequence: ENSG00000294582 ENST00000724516.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 2 publications found

Genes affected

ENSG00000294582 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000724516.1. 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
	ENSG00000294582	ENST00000724516.1		n.169+4104G>A		intron	N/A
	ENSG00000294582	ENST00000724517.1		n.272+4104G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93255 AN: 151980 Hom.: 29524 Cov.: 33

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.614 AC: 93362 AN: 152098 Hom.: 29573 Cov.: 33 AF XY: 0.625 AC XY: 46476 AN XY: 74362

African (AFR) AF: 0.685 AC: 28422 AN: 41494

American (AMR) AF: 0.654 AC: 9986 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1738 AN: 3472

East Asian (EAS) AF: 0.988 AC: 5127 AN: 5188

South Asian (SAS) AF: 0.605 AC: 2922 AN: 4826

European-Finnish (FIN) AF: 0.702 AC: 7421 AN: 10578

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.529 AC: 35933 AN: 67954

Other (OTH) AF: 0.578 AC: 1218 AN: 2106

Alfa AF: 0.596 Hom.: 3751

Bravo AF: 0.616

Asia WGS AF: 0.819 AC: 2848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.66
DANN	Benign	0.41
PhyloP100		-1.3

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: rs6439828;

hg19: chr3-138630594;