rs17019682

Variant names:

• chr12-91911494-A-T
• rs17019682

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 0.0783 in 152,156 control chromosomes in the GnomAD database, including 693 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 0.078 (693 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.710

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.147 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: 0.0782 AC: 11894 AN: 152038 Hom.: 693 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0408

Gnomad ASJ AF: 0.0543

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0389

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0512

Gnomad OTH AF: 0.0614

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

GnomAD4 genome AF: 0.0783 AC: 11907 AN: 152156 Hom.: 693 Cov.: 32 AF XY: 0.0772 AC XY: 5748 AN XY: 74412

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.0408

Gnomad4 ASJ AF: 0.0543

Gnomad4 EAS AF: 0.0143

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.0389

Gnomad4 NFE AF: 0.0512

Gnomad4 OTH AF: 0.0598

Alfa AF: 0.0674 Hom.: 50

Bravo AF: 0.0788

Asia WGS AF: 0.0780 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.4
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17019682; hg19: chr12-92305270;