rs12903150

Variant names:

• chr15-78432303-A-G
• rs12903150

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 0.214 in 152,234 control chromosomes in the GnomAD database, including 4,111 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 0.21 (4111 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.536

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 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: 0.214 AC: 32628 AN: 152116 Hom.: 4108 Cov.: 31

Gnomad AFR AF: 0.0834

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.214 AC: 32613 AN: 152234 Hom.: 4111 Cov.: 31 AF XY: 0.217 AC XY: 16118 AN XY: 74416

Gnomad4 AFR AF: 0.0832

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.209

Alfa AF: 0.259 Hom.: 10853

Bravo AF: 0.207

Asia WGS AF: 0.236 AC: 822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.6
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12903150; hg19: chr15-78724645;