rs3890995

Variant names:

• chr12-109095724-T-C
• rs3890995

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 0.189 in 152,216 control chromosomes in the GnomAD database, including 2,726 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 0.19 (2726 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.596

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 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: 0.189 AC: 28747 AN: 152098 Hom.: 2724 Cov.: 33

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.189 AC: 28752 AN: 152216 Hom.: 2726 Cov.: 33 AF XY: 0.191 AC XY: 14245 AN XY: 74432

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.178

Alfa AF: 0.187 Hom.: 1666

Bravo AF: 0.183

Asia WGS AF: 0.263 AC: 914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.59
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3890995; hg19: chr12-109533529;