12-131608479-G-A

Variant names:

• chr12-131608479-G-A
• rs11609565

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 0.192 in 151,986 control chromosomes in the GnomAD database, including 3,179 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 0.19 (3179 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.351 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: 0.192 AC: 29194 AN: 151868 Hom.: 3176 Cov.: 33

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.192 AC: 29223 AN: 151986 Hom.: 3179 Cov.: 33 AF XY: 0.199 AC XY: 14800 AN XY: 74268

African (AFR) AF: 0.133 AC: 5520 AN: 41458

American (AMR) AF: 0.157 AC: 2395 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 456 AN: 3470

East Asian (EAS) AF: 0.364 AC: 1878 AN: 5156

South Asian (SAS) AF: 0.345 AC: 1661 AN: 4816

European-Finnish (FIN) AF: 0.330 AC: 3475 AN: 10530

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13303 AN: 67950

Other (OTH) AF: 0.170 AC: 358 AN: 2112

Alfa AF: 0.188 Hom.: 4446

Bravo AF: 0.174

Asia WGS AF: 0.355 AC: 1235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.53
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs11609565; hg19: chr12-132093024;