11-60112565-C-T

Variant names:

• chr11-60112565-C-T
• rs540170

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 0.378 in 151,984 control chromosomes in the GnomAD database, including 11,426 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 0.38 (11426 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57430 AN: 151866 Hom.: 11424 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.378 AC: 57448 AN: 151984 Hom.: 11426 Cov.: 32 AF XY: 0.375 AC XY: 27886 AN XY: 74292

African (AFR) AF: 0.277 AC: 11451 AN: 41410

American (AMR) AF: 0.334 AC: 5104 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1599 AN: 3468

East Asian (EAS) AF: 0.376 AC: 1944 AN: 5176

South Asian (SAS) AF: 0.547 AC: 2635 AN: 4818

European-Finnish (FIN) AF: 0.308 AC: 3250 AN: 10568

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30024 AN: 67954

Other (OTH) AF: 0.420 AC: 888 AN: 2112

Alfa AF: 0.411 Hom.: 6530

Bravo AF: 0.371

Asia WGS AF: 0.456 AC: 1587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.49
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs540170; hg19: chr11-59880038;