14-31283458-T-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000257831 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.835

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.978

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.697

Alfa AF: 0.611 Hom.: 44667

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs927704; hg19: chr14-31752664;