14-81627100-C-T

Variant names:

• chr14-81627100-C-T
• rs756019

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.132 AC: 5459 AN: 41430

American (AMR) AF: 0.258 AC: 3933 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 819 AN: 3466

East Asian (EAS) AF: 0.223 AC: 1147 AN: 5148

South Asian (SAS) AF: 0.229 AC: 1100 AN: 4808

European-Finnish (FIN) AF: 0.291 AC: 3074 AN: 10548

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13677 AN: 67930

Other (OTH) AF: 0.192 AC: 405 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.016
DANN	Benign	0.61
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs756019; hg19: chr14-82093444;