14-86435710-C-T

Variant names:

• chr14-86435710-C-T
• rs12882718

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 0.336 in 151,680 control chromosomes in the GnomAD database, including 10,052 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 0.34 (10052 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.313

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 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: 0.336 AC: 50886 AN: 151562 Hom.: 10051 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.336 AC: 50898 AN: 151680 Hom.: 10052 Cov.: 32 AF XY: 0.336 AC XY: 24925 AN XY: 74094

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.363

Alfa AF: 0.397 Hom.: 24388

Bravo AF: 0.339

Asia WGS AF: 0.524 AC: 1819 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12882718; hg19: chr14-86902054;