rs10799599

Variant names:

• chr1-19968007-C-G
• rs10799599

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 0.335 in 152,004 control chromosomes in the GnomAD database, including 9,039 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 0.33 (9039 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.709
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.388 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: 0.335 AC: 50912 AN: 151886 Hom.: 9047 Cov.: 31

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.335 AC: 50911 AN: 152004 Hom.: 9039 Cov.: 31 AF XY: 0.340 AC XY: 25287 AN XY: 74292

African (AFR) AF: 0.232 AC: 9634 AN: 41492

American (AMR) AF: 0.320 AC: 4888 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1199 AN: 3470

East Asian (EAS) AF: 0.289 AC: 1491 AN: 5168

South Asian (SAS) AF: 0.403 AC: 1937 AN: 4810

European-Finnish (FIN) AF: 0.476 AC: 5016 AN: 10536

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25776 AN: 67924

Other (OTH) AF: 0.319 AC: 673 AN: 2110

Alfa AF: 0.342 Hom.: 1126

Bravo AF: 0.319

Asia WGS AF: 0.327 AC: 1136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.8
DANN	Benign	0.70
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs10799599; hg19: chr1-20294500;