rs17117532

Variant names:

• chr14-82856620-C-A
• rs17117532

Your query was ambiguous. Multiple possible variants found:

• chr14-82856620-C-A
• chr14-82856620-C-T

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 0.119 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.172 AC: 7094 AN: 41358

American (AMR) AF: 0.127 AC: 1941 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0622 AC: 216 AN: 3470

East Asian (EAS) AF: 0.124 AC: 641 AN: 5162

South Asian (SAS) AF: 0.0749 AC: 360 AN: 4808

European-Finnish (FIN) AF: 0.110 AC: 1151 AN: 10502

Middle Eastern (MID) AF: 0.0616 AC: 18 AN: 292

European-Non Finnish (NFE) AF: 0.0932 AC: 6330 AN: 67938

Other (OTH) AF: 0.122 AC: 257 AN: 2104

Alfa AF: 0.0970 Hom.: 1515

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
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs17117532; hg19: chr14-83322964;