12-91890525-C-T

Variant names:

• chr12-91890525-C-T
• rs11106325

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 0.253 in 151,914 control chromosomes in the GnomAD database, including 6,683 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 0.25 (6683 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.528
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 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: 0.253 AC: 38399 AN: 151796 Hom.: 6676 Cov.: 32

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.253 AC: 38441 AN: 151914 Hom.: 6683 Cov.: 32 AF XY: 0.250 AC XY: 18586 AN XY: 74240

African (AFR) AF: 0.494 AC: 20463 AN: 41428

American (AMR) AF: 0.144 AC: 2197 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 624 AN: 3466

East Asian (EAS) AF: 0.209 AC: 1080 AN: 5174

South Asian (SAS) AF: 0.333 AC: 1605 AN: 4818

European-Finnish (FIN) AF: 0.158 AC: 1669 AN: 10534

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.148 AC: 10054 AN: 67930

Other (OTH) AF: 0.229 AC: 484 AN: 2110

Alfa AF: 0.100 Hom.: 206

Bravo AF: 0.257

Asia WGS AF: 0.276 AC: 960 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.48
DANN	Benign	0.28
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs11106325; hg19: chr12-92284301;