rs10445823

chr2-219045442-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;