rs10799599

Variant names:

• chr1-19968007-C-G
• rs10799599

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.319

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10799599; hg19: chr1-20294500;