rs10799445

Variant names:

• chr1-227724182-A-C
• rs10799445

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 0.263 in 152,018 control chromosomes in the GnomAD database, including 5,561 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 0.26 (5561 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 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: 0.263 AC: 39921 AN: 151900 Hom.: 5558 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.263 AC: 39939 AN: 152018 Hom.: 5561 Cov.: 32 AF XY: 0.265 AC XY: 19696 AN XY: 74314

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.247

Alfa AF: 0.240 Hom.: 847

Bravo AF: 0.260

Asia WGS AF: 0.174 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.9
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10799445; hg19: chr1-227911883;