rs1113053

Variant names:

• chr12-33007788-A-G
• rs1113053

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 0.141 in 152,180 control chromosomes in the GnomAD database, including 1,532 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 0.14 (1532 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.981
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21370 AN: 152062 Hom.: 1531 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.0810

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.141 AC: 21392 AN: 152180 Hom.: 1532 Cov.: 32 AF XY: 0.140 AC XY: 10440 AN XY: 74404

African (AFR) AF: 0.155 AC: 6434 AN: 41524

American (AMR) AF: 0.117 AC: 1787 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 631 AN: 3470

East Asian (EAS) AF: 0.0812 AC: 420 AN: 5172

South Asian (SAS) AF: 0.121 AC: 584 AN: 4832

European-Finnish (FIN) AF: 0.117 AC: 1245 AN: 10618

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9815 AN: 67968

Other (OTH) AF: 0.142 AC: 300 AN: 2116

Alfa AF: 0.143 Hom.: 835

Bravo AF: 0.140

Asia WGS AF: 0.116 AC: 403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.2
DANN	Benign	0.73
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs1113053; hg19: chr12-33160722;