rs10445823

Variant names:

• chr2-219045442-T-C
• rs10445823

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 0.197 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.0972

Gnomad4 FIN AF: 0.0824

Gnomad4 NFE AF: 0.0987

Gnomad4 OTH AF: 0.190

Alfa AF: 0.116 Hom.: 1938

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10445823; hg19: chr2-219910164;