4-125505540-C-T

Variant names:

• chr4-125505540-C-T
• rs12639834
• ENST00000788000.1:n.301-6162G>A

Variant summary

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

The ENST00000788000.1(ENSG00000302594):​n.301-6162G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 151,780 control chromosomes in the GnomAD database, including 7,834 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 0.30 (7834 hom., cov: 32)
• Consequence: ENSG00000302594 ENST00000788000.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 8 publications found

Genes affected

ENSG00000302594 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302594	ENST00000788000.1	n.301-6162G>A		intron_variant	Intron 2 of 3
ENSG00000302594	ENST00000788001.1	n.*83G>A		downstream_gene_variant
ENSG00000302594	ENST00000788002.1	n.*85G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46041 AN: 151662 Hom.: 7835 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.303 AC: 46060 AN: 151780 Hom.: 7834 Cov.: 32 AF XY: 0.304 AC XY: 22519 AN XY: 74138

African (AFR) AF: 0.135 AC: 5604 AN: 41464

American (AMR) AF: 0.280 AC: 4256 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1143 AN: 3466

East Asian (EAS) AF: 0.375 AC: 1927 AN: 5142

South Asian (SAS) AF: 0.418 AC: 2017 AN: 4820

European-Finnish (FIN) AF: 0.376 AC: 3955 AN: 10508

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.384 AC: 26043 AN: 67858

Other (OTH) AF: 0.324 AC: 678 AN: 2092

Alfa AF: 0.349 Hom.: 28115

Bravo AF: 0.285

Asia WGS AF: 0.392 AC: 1366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.29
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs12639834; hg19: chr4-126426695;