chr14-46613802-T-C

Variant names:

• chr14-46613802-T-C
• rs10139381
• XR_001750753.1:n.813+1315A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001750753.1(LOC105370481):​n.813+1315A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 151,514 control chromosomes in the GnomAD database, including 4,351 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 0.23 (4351 hom., cov: 32)
• Consequence: LOC105370481 XR_001750753.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150
• Publications: 5 publications found

Genes affected

LOC105370481 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35219 AN: 151396 Hom.: 4355 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.0823

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.232 AC: 35214 AN: 151514 Hom.: 4351 Cov.: 32 AF XY: 0.228 AC XY: 16904 AN XY: 74062

African (AFR) AF: 0.185 AC: 7680 AN: 41428

American (AMR) AF: 0.248 AC: 3744 AN: 15122

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1199 AN: 3460

East Asian (EAS) AF: 0.0815 AC: 420 AN: 5152

South Asian (SAS) AF: 0.182 AC: 880 AN: 4822

European-Finnish (FIN) AF: 0.213 AC: 2240 AN: 10518

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.268 AC: 18154 AN: 67708

Other (OTH) AF: 0.243 AC: 511 AN: 2102

Alfa AF: 0.255 Hom.: 2631

Bravo AF: 0.233

Asia WGS AF: 0.159 AC: 545 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	10
DANN	Benign	0.81
PhyloP100		-0.015

Splicing

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

Other links and lift over

dbSNP: rs10139381; hg19: chr14-47083005;