rs12550903

Variant names:

• chr9-75215654-C-T
• rs12550903

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.167 in 152,058 control chromosomes in the GnomAD database, including 2,362 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 0.17 (2362 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.271 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: 0.167 AC: 25338 AN: 151938 Hom.: 2357 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.167 AC: 25355 AN: 152058 Hom.: 2362 Cov.: 32 AF XY: 0.168 AC XY: 12484 AN XY: 74330

African (AFR) AF: 0.100 AC: 4160 AN: 41472

American (AMR) AF: 0.261 AC: 3996 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 479 AN: 3466

East Asian (EAS) AF: 0.284 AC: 1467 AN: 5174

South Asian (SAS) AF: 0.154 AC: 744 AN: 4820

European-Finnish (FIN) AF: 0.153 AC: 1613 AN: 10572

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12448 AN: 67958

Other (OTH) AF: 0.164 AC: 346 AN: 2108

Alfa AF: 0.182 Hom.: 8505

Bravo AF: 0.176

Asia WGS AF: 0.220 AC: 761 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.94
DANN	Benign	0.54
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs12550903; hg19: chr9-77830570;