4-14387731-A-G

Variant names:

• chr4-14387731-A-G
• rs1013284
• ENST00000507932.1:n.428-1598T>C

Variant summary

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

The ENST00000507932.1(ENSG00000251412):​n.428-1598T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,870 control chromosomes in the GnomAD database, including 8,422 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 0.33 (8422 hom., cov: 32)
• Consequence: ENSG00000251412 ENST00000507932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 3 publications found

Genes affected

ENSG00000251412 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.372 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
ENSG00000251412	ENST00000507932.1	n.428-1598T>C		intron_variant	Intron 3 of 5	3
ENSG00000287360	ENST00000654462.1	n.424+27908A>G		intron_variant	Intron 1 of 2
ENSG00000287360	ENST00000723358.1	n.417+27908A>G		intron_variant	Intron 1 of 4
ENSG00000287360	ENST00000723359.1	n.451+27908A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50371 AN: 151752 Hom.: 8404 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.332 AC: 50421 AN: 151870 Hom.: 8422 Cov.: 32 AF XY: 0.331 AC XY: 24549 AN XY: 74184

African (AFR) AF: 0.314 AC: 12994 AN: 41442

American (AMR) AF: 0.367 AC: 5595 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1206 AN: 3470

East Asian (EAS) AF: 0.331 AC: 1705 AN: 5146

South Asian (SAS) AF: 0.386 AC: 1855 AN: 4804

European-Finnish (FIN) AF: 0.282 AC: 2972 AN: 10522

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23017 AN: 67924

Other (OTH) AF: 0.345 AC: 727 AN: 2108

Alfa AF: 0.341 Hom.: 15486

Bravo AF: 0.332

Asia WGS AF: 0.325 AC: 1132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.068
DANN	Benign	0.54
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1013284; hg19: chr4-14389355;