10-122363116-T-C

Variant names:

• chr10-122363116-T-C
• rs7080960

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 0.611 in 152,016 control chromosomes in the GnomAD database, including 29,832 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 0.61 (29832 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.94
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 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: 0.611 AC: 92779 AN: 151898 Hom.: 29777 Cov.: 32

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.611 AC: 92890 AN: 152016 Hom.: 29832 Cov.: 32 AF XY: 0.621 AC XY: 46184 AN XY: 74336

African (AFR) AF: 0.752 AC: 31191 AN: 41466

American (AMR) AF: 0.652 AC: 9975 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1522 AN: 3462

East Asian (EAS) AF: 0.944 AC: 4872 AN: 5162

South Asian (SAS) AF: 0.721 AC: 3474 AN: 4816

European-Finnish (FIN) AF: 0.609 AC: 6425 AN: 10552

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.495 AC: 33648 AN: 67958

Other (OTH) AF: 0.555 AC: 1173 AN: 2112

Alfa AF: 0.531 Hom.: 39086

Bravo AF: 0.623

Asia WGS AF: 0.847 AC: 2944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.28
DANN	Benign	0.77
PhyloP100		-3.9

Splicing

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

Other links and lift over

dbSNP: rs7080960; hg19: chr10-124122632;