14-81627100-C-T

Position:

• chr14-81627100-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 0.197 in 151,902 control chromosomes in the GnomAD database, including 3,168 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 0.20 (3168 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.251 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: 0.197 AC: 29880 AN: 151784 Hom.: 3165 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.197 AC: 29915 AN: 151902 Hom.: 3168 Cov.: 32 AF XY: 0.202 AC XY: 14984 AN XY: 74274

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.192

Alfa AF: 0.193 Hom.: 375

Bravo AF: 0.194

Asia WGS AF: 0.226 AC: 784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.016
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs756019; hg19: chr14-82093444;