rs12231819

Variant names:

• chr12-91069931-A-G
• rs12231819

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 0.167 in 152,040 control chromosomes in the GnomAD database, including 2,639 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 0.17 (2639 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.284 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: 0.167 AC: 25305 AN: 151922 Hom.: 2636 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.0703

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.167 AC: 25341 AN: 152040 Hom.: 2639 Cov.: 32 AF XY: 0.167 AC XY: 12399 AN XY: 74322

African (AFR) AF: 0.288 AC: 11960 AN: 41470

American (AMR) AF: 0.182 AC: 2773 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0703 AC: 244 AN: 3472

East Asian (EAS) AF: 0.134 AC: 691 AN: 5176

South Asian (SAS) AF: 0.210 AC: 1014 AN: 4820

European-Finnish (FIN) AF: 0.108 AC: 1140 AN: 10566

Middle Eastern (MID) AF: 0.113 AC: 33 AN: 292

European-Non Finnish (NFE) AF: 0.104 AC: 7094 AN: 67956

Other (OTH) AF: 0.143 AC: 303 AN: 2112

Alfa AF: 0.137 Hom.: 1168

Bravo AF: 0.180

Asia WGS AF: 0.193 AC: 665 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.75
PhyloP100		-0.035

Splicing

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

Other links and lift over

dbSNP: rs12231819; hg19: chr12-91463708;