14-31283458-T-G

Variant names:

• chr14-31283458-T-G
• rs927704
• ENST00000551799.1:n.400+4324T>G

Variant summary

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

The ENST00000551799.1(ENSG00000257831):​n.400+4324T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 151,914 control chromosomes in the GnomAD database, including 38,400 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 0.70 (38400 hom., cov: 30)
• Consequence: ENSG00000257831 ENST00000551799.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.357
• Publications: 4 publications found

Genes affected

ENSG00000257831 (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 (EAS) allele frequency at 95% confidence interval = 0.955 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
ENSG00000257831	ENST00000551799.1	n.400+4324T>G		intron_variant	Intron 4 of 5	3

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106277 AN: 151796 Hom.: 38356 Cov.: 30

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.700 AC: 106386 AN: 151914 Hom.: 38400 Cov.: 30 AF XY: 0.706 AC XY: 52430 AN XY: 74230

African (AFR) AF: 0.835 AC: 34609 AN: 41448

American (AMR) AF: 0.724 AC: 11042 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2107 AN: 3470

East Asian (EAS) AF: 0.978 AC: 5038 AN: 5152

South Asian (SAS) AF: 0.813 AC: 3908 AN: 4806

European-Finnish (FIN) AF: 0.654 AC: 6882 AN: 10522

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40618 AN: 67948

Other (OTH) AF: 0.697 AC: 1468 AN: 2106

Alfa AF: 0.626 Hom.: 108799

Bravo AF: 0.712

Asia WGS AF: 0.895 AC: 3111 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	5.2
DANN	Benign	0.67
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs927704; hg19: chr14-31752664;