14-30791724-C-T

Position:

• chr14-30791724-C-T

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 0.0136 in 152,122 control chromosomes in the GnomAD database, including 32 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 0.014 (32 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.550

Genes affected

(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 (EAS) allele frequency at 95% confidence interval = 0.0666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.30791724C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000258558	ENST00000554665.1	n.209-9728G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0136 AC: 2062 AN: 152002 Hom.: 32 Cov.: 31

Gnomad AFR AF: 0.0133

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00989

Gnomad ASJ AF: 0.00952

Gnomad EAS AF: 0.0721

Gnomad SAS AF: 0.0547

Gnomad FIN AF: 0.000189

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.00925

Gnomad OTH AF: 0.0235

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

GnomAD4 genome AF: 0.0136 AC: 2065 AN: 152122 Hom.: 32 Cov.: 31 AF XY: 0.0145 AC XY: 1075 AN XY: 74370

Gnomad4 AFR AF: 0.0133

Gnomad4 AMR AF: 0.00988

Gnomad4 ASJ AF: 0.00952

Gnomad4 EAS AF: 0.0726

Gnomad4 SAS AF: 0.0547

Gnomad4 FIN AF: 0.000189

Gnomad4 NFE AF: 0.00925

Gnomad4 OTH AF: 0.0228

Alfa AF: 0.0122 Hom.: 17

Bravo AF: 0.0136

Asia WGS AF: 0.0730 AC: 254 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	1.8
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483362; hg19: chr14-31260930;