12-91059593-A-C

Variant names:

• chr12-91059593-A-C
• rs17018627

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 0.102 in 151,114 control chromosomes in the GnomAD database, including 948 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 0.10 (948 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• 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: 0.102 AC: 15341 AN: 150996 Hom.: 943 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0757

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0700

Gnomad SAS AF: 0.0409

Gnomad FIN AF: 0.0488

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.0966

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

GnomAD4 genome AF: 0.102 AC: 15366 AN: 151114 Hom.: 948 Cov.: 32 AF XY: 0.0987 AC XY: 7290 AN XY: 73828

African (AFR) AF: 0.171 AC: 7076 AN: 41308

American (AMR) AF: 0.0756 AC: 1143 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 513 AN: 3440

East Asian (EAS) AF: 0.0700 AC: 357 AN: 5102

South Asian (SAS) AF: 0.0409 AC: 197 AN: 4812

European-Finnish (FIN) AF: 0.0488 AC: 517 AN: 10586

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.0782 AC: 5274 AN: 67454

Other (OTH) AF: 0.0999 AC: 209 AN: 2092

Alfa AF: 0.0689 Hom.: 229

Bravo AF: 0.108

Asia WGS AF: 0.0590 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.69
DANN	Benign	0.56
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs17018627; hg19: chr12-91453370;