chr14-25243094-G-A

Position:

• chr14-25243094-G-A

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 0.333 in 151,876 control chromosomes in the GnomAD database, including 9,747 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 0.33 (9747 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.577

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.522 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: 0.333 AC: 50503 AN: 151758 Hom.: 9750 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.333 AC: 50505 AN: 151876 Hom.: 9747 Cov.: 32 AF XY: 0.331 AC XY: 24576 AN XY: 74192

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.386

Alfa AF: 0.404 Hom.: 16947

Bravo AF: 0.334

Asia WGS AF: 0.339 AC: 1179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.9
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1461549; hg19: chr14-25712300;