14-28018670-A-T

Variant names:

• chr14-28018670-A-T
• rs877726

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 0.267 in 152,058 control chromosomes in the GnomAD database, including 5,768 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 0.27 (5768 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.424
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 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: 0.267 AC: 40601 AN: 151940 Hom.: 5777 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.267 AC: 40598 AN: 152058 Hom.: 5768 Cov.: 32 AF XY: 0.267 AC XY: 19868 AN XY: 74308

African (AFR) AF: 0.284 AC: 11775 AN: 41482

American (AMR) AF: 0.213 AC: 3264 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 828 AN: 3460

East Asian (EAS) AF: 0.580 AC: 2983 AN: 5142

South Asian (SAS) AF: 0.323 AC: 1552 AN: 4804

European-Finnish (FIN) AF: 0.247 AC: 2617 AN: 10588

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.246 AC: 16727 AN: 67976

Other (OTH) AF: 0.261 AC: 551 AN: 2114

Alfa AF: 0.243 Hom.: 566

Bravo AF: 0.266

Asia WGS AF: 0.406 AC: 1410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.76
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs877726; hg19: chr14-28487876;