rs10799599

Positions:

• chr1-19968007-C-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;