14-31283458-T-G

Position:

• chr14-31283458-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.357

Genes affected

(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/exons	MANE	Protein	UniProt
		n.31283458T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000257831	ENST00000551799.1	n.400+4324T>G		intron_variant		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;