rs11833579

Positions:

• chr12-666033-G-A
• chr12-666033-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.255 in 151,392 control chromosomes in the GnomAD database, including 5,063 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 0.26 (5063 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38618 AN: 151286 Hom.: 5061 Cov.: 31

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.255 AC: 38633 AN: 151392 Hom.: 5063 Cov.: 31 AF XY: 0.259 AC XY: 19117 AN XY: 73904

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.278

Alfa AF: 0.237 Hom.: 2087

Bravo AF: 0.259

Asia WGS AF: 0.313 AC: 1085 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.32
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11833579; hg19: chr12-775199;