5-14120477-C-T

Variant names:

• chr5-14120477-C-T
• rs348116

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 0.102 in 152,202 control chromosomes in the GnomAD database, including 1,063 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 (1063 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.185 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: 15486 AN: 152084 Hom.: 1059 Cov.: 33

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0818

Gnomad ASJ AF: 0.0332

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.0981

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0521

Gnomad OTH AF: 0.0898

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

GnomAD4 genome AF: 0.102 AC: 15504 AN: 152202 Hom.: 1063 Cov.: 33 AF XY: 0.106 AC XY: 7877 AN XY: 74404

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.0818

Gnomad4 ASJ AF: 0.0332

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.0980

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0521

Gnomad4 OTH AF: 0.0888

Alfa AF: 0.0819 Hom.: 95

Bravo AF: 0.104

Asia WGS AF: 0.139 AC: 483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.14
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs348116; hg19: chr5-14120586;