rs10189905

Variant names:

• chr2-198814386-T-G
• rs10189905

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;