14-42719707-C-T

Position:

• chr14-42719707-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.738 in 151,922 control chromosomes in the GnomAD database, including 41,786 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 0.74 (41786 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.458

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.762 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: 0.738 AC: 111966 AN: 151804 Hom.: 41751 Cov.: 31

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.738 AC: 112057 AN: 151922 Hom.: 41786 Cov.: 31 AF XY: 0.738 AC XY: 54774 AN XY: 74218

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.726

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.721

Alfa AF: 0.756 Hom.: 26410

Bravo AF: 0.725

Asia WGS AF: 0.654 AC: 2277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	18
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1777077; hg19: chr14-43188910;