11-60545390-C-T

Variant names:

• chr11-60545390-C-T
• rs1941027

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 0.9 in 152,218 control chromosomes in the GnomAD database, including 62,418 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 0.90 (62418 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.900 AC: 136861 AN: 152100 Hom.: 62405 Cov.: 32

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.950

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.956

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.964

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.900 AC: 136927 AN: 152218 Hom.: 62418 Cov.: 32 AF XY: 0.902 AC XY: 67168 AN XY: 74432

African (AFR) AF: 0.733 AC: 30400 AN: 41488

American (AMR) AF: 0.949 AC: 14504 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.950 AC: 3296 AN: 3470

East Asian (EAS) AF: 0.997 AC: 5166 AN: 5184

South Asian (SAS) AF: 0.956 AC: 4610 AN: 4824

European-Finnish (FIN) AF: 0.967 AC: 10263 AN: 10614

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.964 AC: 65597 AN: 68028

Other (OTH) AF: 0.920 AC: 1945 AN: 2114

Alfa AF: 0.917 Hom.: 21318

Bravo AF: 0.889

Asia WGS AF: 0.948 AC: 3297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	9.0
DANN	Benign	0.67
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs1941027; hg19: chr11-60312863;