chr14-28552722-C-T

Position:

• chr14-28552722-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 0.376 in 151,832 control chromosomes in the GnomAD database, including 11,027 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 0.38 (11027 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

ACMG classification

Verdict is Benign. Variant got -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 = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57054 AN: 151716 Hom.: 11020 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.376 AC: 57081 AN: 151832 Hom.: 11027 Cov.: 32 AF XY: 0.372 AC XY: 27595 AN XY: 74186

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.409

Alfa AF: 0.405 Hom.: 18197

Bravo AF: 0.371

Asia WGS AF: 0.245 AC: 848 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7493138; hg19: chr14-29021928;