chr11-60085123-C-T

Variant names:

• chr11-60085123-C-T
• rs12361312

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 0.161 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0441 AC: 1828 AN: 41442

American (AMR) AF: 0.148 AC: 2263 AN: 15260

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

East Asian (EAS) AF: 0.101 AC: 521 AN: 5178

South Asian (SAS) AF: 0.107 AC: 515 AN: 4808

European-Finnish (FIN) AF: 0.239 AC: 2515 AN: 10524

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15519 AN: 67944

Other (OTH) AF: 0.179 AC: 377 AN: 2108

Alfa AF: 0.197 Hom.: 7421

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
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs12361312; hg19: chr11-59852596;