rs17117532

Positions:

• chr14-82856620-C-A
• chr14-82856620-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 0.119 in 151,796 control chromosomes in the GnomAD database, including 1,210 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 0.12 (1210 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 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: 0.119 AC: 18114 AN: 151680 Hom.: 1202 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0622

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.0756

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0932

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.119 AC: 18137 AN: 151796 Hom.: 1210 Cov.: 32 AF XY: 0.120 AC XY: 8903 AN XY: 74186

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.0622

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.0749

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.0932

Gnomad4 OTH AF: 0.122

Alfa AF: 0.0941 Hom.: 1033

Bravo AF: 0.125

Asia WGS AF: 0.0990 AC: 345 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17117532; hg19: chr14-83322964;