4-14387731-A-G

Position:

• chr4-14387731-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000251412 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000251412	ENST00000507932.1	n.428-1598T>C		intron_variant		3
ENSG00000287360	ENST00000654462.1	n.424+27908A>G		intron_variant

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

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.345

Alfa AF: 0.343 Hom.: 12476

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1013284; hg19: chr4-14389355;