chr14-86308051-G-T

Variant names:

• chr14-86308051-G-T
• rs10133064

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 0.102 in 152,176 control chromosomes in the GnomAD database, including 1,030 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 0.10 (1030 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 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: 0.102 AC: 15539 AN: 152054 Hom.: 1028 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0677

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.0996

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0700

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.102 AC: 15551 AN: 152176 Hom.: 1030 Cov.: 32 AF XY: 0.104 AC XY: 7755 AN XY: 74400

African (AFR) AF: 0.117 AC: 4872 AN: 41514

American (AMR) AF: 0.143 AC: 2190 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0677 AC: 235 AN: 3470

East Asian (EAS) AF: 0.336 AC: 1734 AN: 5156

South Asian (SAS) AF: 0.0942 AC: 454 AN: 4822

European-Finnish (FIN) AF: 0.0996 AC: 1055 AN: 10594

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0700 AC: 4759 AN: 68012

Other (OTH) AF: 0.0984 AC: 208 AN: 2114

Alfa AF: 0.0819 Hom.: 2684

Bravo AF: 0.109

Asia WGS AF: 0.190 AC: 657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.30
PhyloP100		-0.054

Splicing

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

Other links and lift over

dbSNP: rs10133064; hg19: chr14-86774395;