rs17103124

Variant names:

• chr14-65951314-C-T
• rs17103124

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 0.168 in 152,052 control chromosomes in the GnomAD database, including 2,488 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 0.17 (2488 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411

ACMG classification

Verdict is Benign. Variant got -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 = 0.262 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: 0.168 AC: 25526 AN: 151934 Hom.: 2488 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.0688

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0813

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.168 AC: 25545 AN: 152052 Hom.: 2488 Cov.: 32 AF XY: 0.164 AC XY: 12227 AN XY: 74332

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.0691

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0813

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.180

Alfa AF: 0.147 Hom.: 2450

Bravo AF: 0.177

Asia WGS AF: 0.121 AC: 423 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	7.9
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17103124; hg19: chr14-66418032;