rs10445823

Variant names:

• chr2-219045442-T-C
• rs10445823

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 0.197 in 151,640 control chromosomes in the GnomAD database, including 4,642 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 0.20 (4642 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.778
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.436 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: 0.197 AC: 29890 AN: 151522 Hom.: 4623 Cov.: 30

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0973

Gnomad FIN AF: 0.0824

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0986

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.197 AC: 29948 AN: 151640 Hom.: 4642 Cov.: 30 AF XY: 0.193 AC XY: 14265 AN XY: 74096

African (AFR) AF: 0.441 AC: 18184 AN: 41224

American (AMR) AF: 0.135 AC: 2064 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 378 AN: 3468

East Asian (EAS) AF: 0.146 AC: 754 AN: 5170

South Asian (SAS) AF: 0.0972 AC: 467 AN: 4804

European-Finnish (FIN) AF: 0.0824 AC: 867 AN: 10522

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0987 AC: 6698 AN: 67894

Other (OTH) AF: 0.190 AC: 398 AN: 2100

Alfa AF: 0.127 Hom.: 3062

Bravo AF: 0.213

Asia WGS AF: 0.168 AC: 583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.73
DANN	Benign	0.34
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs10445823; hg19: chr2-219910164;