rs10799445

Variant names:

• chr1-227724182-A-C
• rs10799445

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 0.263 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
• Publications: 37 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.345 AC: 14282 AN: 41448

American (AMR) AF: 0.228 AC: 3481 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 540 AN: 3470

East Asian (EAS) AF: 0.145 AC: 751 AN: 5174

South Asian (SAS) AF: 0.239 AC: 1150 AN: 4812

European-Finnish (FIN) AF: 0.295 AC: 3107 AN: 10542

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15799 AN: 67972

Other (OTH) AF: 0.247 AC: 521 AN: 2112

Alfa AF: 0.235 Hom.: 1950

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
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs10799445; hg19: chr1-227911883;