chr11-60860110-C-T

Variant names:

• chr11-60860110-C-T
• rs533116

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 0.28 in 152,284 control chromosomes in the GnomAD database, including 6,918 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 0.28 (6918 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 11 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 (NFE) allele frequency at 95% confidence interval = 0.371 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: 0.280 AC: 42581 AN: 152164 Hom.: 6915 Cov.: 34

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.0721

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.280 AC: 42594 AN: 152284 Hom.: 6918 Cov.: 34 AF XY: 0.275 AC XY: 20459 AN XY: 74448

African (AFR) AF: 0.133 AC: 5541 AN: 41566

American (AMR) AF: 0.258 AC: 3945 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1459 AN: 3472

East Asian (EAS) AF: 0.0717 AC: 372 AN: 5188

South Asian (SAS) AF: 0.225 AC: 1088 AN: 4826

European-Finnish (FIN) AF: 0.332 AC: 3518 AN: 10600

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.375 AC: 25476 AN: 68008

Other (OTH) AF: 0.311 AC: 658 AN: 2116

Alfa AF: 0.339 Hom.: 2317

Bravo AF: 0.267

Asia WGS AF: 0.148 AC: 515 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	3.3
DANN	Benign	0.65
PhyloP100		0.061

Splicing

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

Other links and lift over

dbSNP: rs533116; hg19: chr11-60627583;