12-91911494-A-T

Variant names:

• chr12-91911494-A-T
• rs17019682

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 0.0783 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.150 AC: 6225 AN: 41478

American (AMR) AF: 0.0408 AC: 623 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0543 AC: 188 AN: 3462

East Asian (EAS) AF: 0.0143 AC: 74 AN: 5174

South Asian (SAS) AF: 0.152 AC: 733 AN: 4822

European-Finnish (FIN) AF: 0.0389 AC: 413 AN: 10610

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0512 AC: 3480 AN: 68008

Other (OTH) AF: 0.0598 AC: 126 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.4
DANN	Benign	0.74
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs17019682; hg19: chr12-92305270;