chr14-25243094-G-A

Variant names:

• chr14-25243094-G-A
• rs1461549

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 0.333 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.122 AC: 5038 AN: 41446

American (AMR) AF: 0.420 AC: 6408 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1631 AN: 3464

East Asian (EAS) AF: 0.539 AC: 2779 AN: 5156

South Asian (SAS) AF: 0.302 AC: 1453 AN: 4810

European-Finnish (FIN) AF: 0.351 AC: 3688 AN: 10518

Middle Eastern (MID) AF: 0.476 AC: 138 AN: 290

European-Non Finnish (NFE) AF: 0.415 AC: 28170 AN: 67922

Other (OTH) AF: 0.386 AC: 812 AN: 2104

Alfa AF: 0.396 Hom.: 20883

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
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs1461549; hg19: chr14-25712300;