rs17103124

Variant names:

• chr14-65951314-C-T
• rs17103124

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.266 AC: 11014 AN: 41442

American (AMR) AF: 0.141 AC: 2152 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 648 AN: 3470

East Asian (EAS) AF: 0.0691 AC: 357 AN: 5166

South Asian (SAS) AF: 0.149 AC: 716 AN: 4802

European-Finnish (FIN) AF: 0.0813 AC: 861 AN: 10588

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9251 AN: 67982

Other (OTH) AF: 0.180 AC: 379 AN: 2108

Alfa AF: 0.151 Hom.: 3901

Bravo AF: 0.177

Asia WGS AF: 0.121 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	7.9
DANN	Benign	0.71
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs17103124; hg19: chr14-66418032;