14-93849429-C-T

Variant names:

• chr14-93849429-C-T
• rs10139611

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 0.126 in 152,116 control chromosomes in the GnomAD database, including 2,459 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 0.13 (2459 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 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: 0.126 AC: 19123 AN: 151998 Hom.: 2459 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0741

Gnomad ASJ AF: 0.0369

Gnomad EAS AF: 0.0355

Gnomad SAS AF: 0.0493

Gnomad FIN AF: 0.0153

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0482

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.126 AC: 19149 AN: 152116 Hom.: 2459 Cov.: 32 AF XY: 0.121 AC XY: 8974 AN XY: 74380

African (AFR) AF: 0.330 AC: 13691 AN: 41426

American (AMR) AF: 0.0740 AC: 1131 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0369 AC: 128 AN: 3468

East Asian (EAS) AF: 0.0355 AC: 184 AN: 5178

South Asian (SAS) AF: 0.0495 AC: 239 AN: 4824

European-Finnish (FIN) AF: 0.0153 AC: 162 AN: 10610

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0482 AC: 3280 AN: 68006

Other (OTH) AF: 0.114 AC: 241 AN: 2114

Alfa AF: 0.0858 Hom.: 1847

Bravo AF: 0.140

Asia WGS AF: 0.0700 AC: 243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.79
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs10139611; hg19: chr14-94315775;