rs1449725

Positions:

• chr14-38707617-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 0.357 in 151,958 control chromosomes in the GnomAD database, including 10,277 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 0.36 (10277 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54213 AN: 151840 Hom.: 10266 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.357 AC: 54262 AN: 151958 Hom.: 10277 Cov.: 32 AF XY: 0.359 AC XY: 26662 AN XY: 74278

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.359

Alfa AF: 0.373 Hom.: 1733

Bravo AF: 0.352

Asia WGS AF: 0.423 AC: 1469 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.32
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1449725; hg19: chr14-39176821;