rs12900333

Positions:

• chr15-78385934-C-T

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 0.0838 in 152,182 control chromosomes in the GnomAD database, including 643 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 0.084 (643 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0838 AC: 12748 AN: 152064 Hom.: 644 Cov.: 32

Gnomad AFR AF: 0.0504

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0758

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.0874

Gnomad SAS AF: 0.0504

Gnomad FIN AF: 0.0587

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0794

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

GnomAD4 genome AF: 0.0838 AC: 12754 AN: 152182 Hom.: 643 Cov.: 32 AF XY: 0.0800 AC XY: 5949 AN XY: 74386

Gnomad4 AFR AF: 0.0504

Gnomad4 AMR AF: 0.0756

Gnomad4 ASJ AF: 0.0986

Gnomad4 EAS AF: 0.0872

Gnomad4 SAS AF: 0.0513

Gnomad4 FIN AF: 0.0587

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.0791

Alfa AF: 0.106 Hom.: 995

Bravo AF: 0.0850

Asia WGS AF: 0.0540 AC: 187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12900333; hg19: chr15-78678276;