11-100558074-C-T

Variant names:

• chr11-100558074-C-T
• rs1502277

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 0.711 in 151,970 control chromosomes in the GnomAD database, including 38,777 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 0.71 (38777 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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: 0.711 AC: 107904 AN: 151852 Hom.: 38750 Cov.: 31

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.790

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.711 AC: 107986 AN: 151970 Hom.: 38777 Cov.: 31 AF XY: 0.715 AC XY: 53118 AN XY: 74248

African (AFR) AF: 0.697 AC: 28859 AN: 41412

American (AMR) AF: 0.757 AC: 11568 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2645 AN: 3472

East Asian (EAS) AF: 0.995 AC: 5142 AN: 5168

South Asian (SAS) AF: 0.824 AC: 3967 AN: 4814

European-Finnish (FIN) AF: 0.694 AC: 7311 AN: 10530

Middle Eastern (MID) AF: 0.791 AC: 231 AN: 292

European-Non Finnish (NFE) AF: 0.681 AC: 46298 AN: 67982

Other (OTH) AF: 0.699 AC: 1476 AN: 2112

Alfa AF: 0.644 Hom.: 2678

Bravo AF: 0.714

Asia WGS AF: 0.867 AC: 3014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.17
DANN	Benign	0.50
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1502277; hg19: chr11-100428805;