rs10777287

Variant names:

• chr12-91075973-C-T
• rs10777287

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 0.764 in 152,030 control chromosomes in the GnomAD database, including 45,748 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 0.76 (45748 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.764 AC: 116074 AN: 151912 Hom.: 45735 Cov.: 33

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.764 AC: 116123 AN: 152030 Hom.: 45748 Cov.: 33 AF XY: 0.772 AC XY: 57380 AN XY: 74326

African (AFR) AF: 0.547 AC: 22671 AN: 41432

American (AMR) AF: 0.828 AC: 12635 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2759 AN: 3472

East Asian (EAS) AF: 0.923 AC: 4775 AN: 5176

South Asian (SAS) AF: 0.932 AC: 4498 AN: 4824

European-Finnish (FIN) AF: 0.897 AC: 9481 AN: 10568

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.835 AC: 56738 AN: 67978

Other (OTH) AF: 0.779 AC: 1643 AN: 2108

Alfa AF: 0.806 Hom.: 122748

Bravo AF: 0.746

Asia WGS AF: 0.898 AC: 3106 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.31
DANN	Benign	0.58
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs10777287; hg19: chr12-91469750;