rs12361312

Positions:

• chr11-60085123-C-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 0.161 in 151,940 control chromosomes in the GnomAD database, including 2,513 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 0.16 (2513 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.225 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: 0.161 AC: 24519 AN: 151822 Hom.: 2512 Cov.: 30

Gnomad AFR AF: 0.0443

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.161 AC: 24521 AN: 151940 Hom.: 2513 Cov.: 30 AF XY: 0.159 AC XY: 11796 AN XY: 74266

Gnomad4 AFR AF: 0.0441

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.179

Alfa AF: 0.199 Hom.: 2032

Bravo AF: 0.151

Asia WGS AF: 0.0940 AC: 326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.3
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12361312; hg19: chr11-59852596;