14-39007303-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 0.874 in 152,156 control chromosomes in the GnomAD database, including 58,300 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 0.87 (58300 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.699

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.874 AC: 132858 AN: 152038 Hom.: 58262 Cov.: 31

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.892

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.874 AC: 132948 AN: 152156 Hom.: 58300 Cov.: 31 AF XY: 0.869 AC XY: 64654 AN XY: 74358

Gnomad4 AFR AF: 0.901

Gnomad4 AMR AF: 0.834

Gnomad4 ASJ AF: 0.845

Gnomad4 EAS AF: 0.972

Gnomad4 SAS AF: 0.700

Gnomad4 FIN AF: 0.892

Gnomad4 NFE AF: 0.871

Gnomad4 OTH AF: 0.846

Alfa AF: 0.860 Hom.: 32709

Bravo AF: 0.875

Asia WGS AF: 0.835 AC: 2908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.9
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8014021; hg19: chr14-39476507;