rs10189905

chr2-198814386-T-G

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 0.121 in 151,634 control chromosomes in the GnomAD database, including 1,354 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 0.12 (1354 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.750

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.202 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: 0.121 AC: 18376 AN: 151520 Hom.: 1350 Cov.: 31

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0948

Gnomad SAS AF: 0.0868

Gnomad FIN AF: 0.0589

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.0857

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.121 AC: 18396 AN: 151634 Hom.: 1354 Cov.: 31 AF XY: 0.118 AC XY: 8725 AN XY: 74098

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.0950

Gnomad4 SAS AF: 0.0869

Gnomad4 FIN AF: 0.0589

Gnomad4 NFE AF: 0.0857

Gnomad4 OTH AF: 0.124

Alfa AF: 0.0949 Hom.: 1270

Bravo AF: 0.131

Asia WGS AF: 0.106 AC: 370 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	11
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10189905; hg19: chr2-199679110;