10-93079885-G-A

Variant names:

• chr10-93079885-G-A
• rs2068888

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 0.427 in 152,010 control chromosomes in the GnomAD database, including 14,859 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 0.43 (14859 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.888
• Publications: 113 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 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: 0.427 AC: 64903 AN: 151892 Hom.: 14873 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.427 AC: 64883 AN: 152010 Hom.: 14859 Cov.: 32 AF XY: 0.434 AC XY: 32265 AN XY: 74300

African (AFR) AF: 0.287 AC: 11909 AN: 41470

American (AMR) AF: 0.461 AC: 7039 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1718 AN: 3470

East Asian (EAS) AF: 0.784 AC: 4032 AN: 5142

South Asian (SAS) AF: 0.647 AC: 3121 AN: 4824

European-Finnish (FIN) AF: 0.452 AC: 4778 AN: 10564

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30906 AN: 67946

Other (OTH) AF: 0.434 AC: 917 AN: 2114

Alfa AF: 0.453 Hom.: 75552

Bravo AF: 0.419

Asia WGS AF: 0.648 AC: 2256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.2
DANN	Benign	0.80
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs2068888; hg19: chr10-94839642;