11-60864668-C-T

Variant names:

• chr11-60864668-C-T
• rs530880

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 0.194 in 151,976 control chromosomes in the GnomAD database, including 3,733 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 0.19 (3733 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.281 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: 0.194 AC: 29455 AN: 151858 Hom.: 3731 Cov.: 32

Gnomad AFR AF: 0.0519

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.0443

Gnomad SAS AF: 0.0836

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.194 AC: 29457 AN: 151976 Hom.: 3733 Cov.: 32 AF XY: 0.187 AC XY: 13902 AN XY: 74298

Gnomad4 AFR AF: 0.0518

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.0440

Gnomad4 SAS AF: 0.0848

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.223

Alfa AF: 0.237 Hom.: 798

Bravo AF: 0.187

Asia WGS AF: 0.0680 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs530880; hg19: chr11-60632141;