10-79900599-A-G

Variant names:

• chr10-79900599-A-G
• rs2250992

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 0.271 in 152,082 control chromosomes in the GnomAD database, including 6,830 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 0.27 (6830 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 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: 0.271 AC: 41133 AN: 151964 Hom.: 6828 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.271 AC: 41149 AN: 152082 Hom.: 6830 Cov.: 32 AF XY: 0.277 AC XY: 20563 AN XY: 74342

African (AFR) AF: 0.133 AC: 5537 AN: 41492

American (AMR) AF: 0.225 AC: 3441 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 979 AN: 3464

East Asian (EAS) AF: 0.757 AC: 3918 AN: 5176

South Asian (SAS) AF: 0.435 AC: 2090 AN: 4808

European-Finnish (FIN) AF: 0.315 AC: 3329 AN: 10562

Middle Eastern (MID) AF: 0.276 AC: 80 AN: 290

European-Non Finnish (NFE) AF: 0.309 AC: 20996 AN: 67970

Other (OTH) AF: 0.257 AC: 543 AN: 2112

Alfa AF: 0.285 Hom.: 3987

Bravo AF: 0.255

Asia WGS AF: 0.530 AC: 1838 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.9
DANN	Benign	0.44
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs2250992; hg19: chr10-81660355;