rs17103124

Positions:

• chr14-65951314-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;