14-94628060-C-T

Position:

• chr14-94628060-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 0.698 in 151,822 control chromosomes in the GnomAD database, including 37,335 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 (37335 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292

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 = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.698 AC: 105942 AN: 151704 Hom.: 37311 Cov.: 29

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.698 AC: 106018 AN: 151822 Hom.: 37335 Cov.: 29 AF XY: 0.696 AC XY: 51618 AN XY: 74190

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.761

Gnomad4 EAS AF: 0.892

Gnomad4 SAS AF: 0.708

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.721

Gnomad4 OTH AF: 0.697

Alfa AF: 0.712 Hom.: 48477

Bravo AF: 0.690

Asia WGS AF: 0.807 AC: 2805 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	1.1
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8005845; hg19: chr14-95094397;