14-83103740-C-T

Variant names:

• chr14-83103740-C-T
• rs10484146

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 0.0512 in 152,128 control chromosomes in the GnomAD database, including 273 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 0.051 (273 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.074 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: 0.0513 AC: 7793 AN: 152010 Hom.: 273 Cov.: 32

Gnomad AFR AF: 0.0140

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0388

Gnomad ASJ AF: 0.0602

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0626

Gnomad FIN AF: 0.0685

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0758

Gnomad OTH AF: 0.0540

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

GnomAD4 genome AF: 0.0512 AC: 7789 AN: 152128 Hom.: 273 Cov.: 32 AF XY: 0.0500 AC XY: 3720 AN XY: 74362

Gnomad4 AFR AF: 0.0139

Gnomad4 AMR AF: 0.0388

Gnomad4 ASJ AF: 0.0602

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0620

Gnomad4 FIN AF: 0.0685

Gnomad4 NFE AF: 0.0758

Gnomad4 OTH AF: 0.0534

Alfa AF: 0.0569 Hom.: 120

Bravo AF: 0.0478

Asia WGS AF: 0.0250 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.47
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484146; hg19: chr14-83570084;