10-80121266-G-A

Variant names:

• chr10-80121266-G-A
• rs4399277

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 0.0873 in 152,118 control chromosomes in the GnomAD database, including 656 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 0.087 (656 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0872 AC: 13254 AN: 152000 Hom.: 649 Cov.: 33

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0672

Gnomad AMR AF: 0.0461

Gnomad ASJ AF: 0.0597

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0276

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0791

Gnomad OTH AF: 0.0723

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

GnomAD4 genome AF: 0.0873 AC: 13284 AN: 152118 Hom.: 656 Cov.: 33 AF XY: 0.0867 AC XY: 6451 AN XY: 74386

African (AFR) AF: 0.128 AC: 5312 AN: 41492

American (AMR) AF: 0.0461 AC: 704 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0597 AC: 207 AN: 3470

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5176

South Asian (SAS) AF: 0.0268 AC: 129 AN: 4822

European-Finnish (FIN) AF: 0.125 AC: 1316 AN: 10570

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0791 AC: 5381 AN: 68000

Other (OTH) AF: 0.0716 AC: 151 AN: 2110

Alfa AF: 0.0856 Hom.: 193

Bravo AF: 0.0825

Asia WGS AF: 0.0220 AC: 77 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.63
PhyloP100		-0.054

Splicing

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

Other links and lift over

dbSNP: rs4399277; hg19: chr10-81881022;