14-28015715-C-T

Variant names:

• chr14-28015715-C-T
• rs2807822

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 0.391 in 151,872 control chromosomes in the GnomAD database, including 12,368 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 0.39 (12368 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.785
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59273 AN: 151754 Hom.: 12366 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.391 AC: 59311 AN: 151872 Hom.: 12368 Cov.: 32 AF XY: 0.395 AC XY: 29307 AN XY: 74204

African (AFR) AF: 0.259 AC: 10736 AN: 41440

American (AMR) AF: 0.359 AC: 5475 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1652 AN: 3466

East Asian (EAS) AF: 0.281 AC: 1448 AN: 5154

South Asian (SAS) AF: 0.454 AC: 2181 AN: 4806

European-Finnish (FIN) AF: 0.535 AC: 5628 AN: 10520

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.454 AC: 30823 AN: 67914

Other (OTH) AF: 0.402 AC: 847 AN: 2108

Alfa AF: 0.433 Hom.: 41314

Bravo AF: 0.372

Asia WGS AF: 0.373 AC: 1299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.66
DANN	Benign	0.39
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs2807822; hg19: chr14-28484921;