rs933890

Variant names:

• chr12-108045145-T-C
• rs933890

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.142 in 152,252 control chromosomes in the GnomAD database, including 1,929 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 0.14 (1929 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.862

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 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: 0.142 AC: 21651 AN: 152134 Hom.: 1928 Cov.: 32

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0518

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.142 AC: 21653 AN: 152252 Hom.: 1929 Cov.: 32 AF XY: 0.136 AC XY: 10100 AN XY: 74444

Gnomad4 AFR AF: 0.0700

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0525

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.159

Alfa AF: 0.166 Hom.: 355

Bravo AF: 0.145

Asia WGS AF: 0.0330 AC: 117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	18
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs933890; hg19: chr12-108438922;