rs12554686

Variant names:

• chr9-21138434-G-A
• rs12554686

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 0.348 in 151,940 control chromosomes in the GnomAD database, including 9,782 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 0.35 (9782 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 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: 0.348 AC: 52910 AN: 151822 Hom.: 9777 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.348 AC: 52933 AN: 151940 Hom.: 9782 Cov.: 32 AF XY: 0.352 AC XY: 26144 AN XY: 74248

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.381

Alfa AF: 0.339 Hom.: 1160

Bravo AF: 0.361

Asia WGS AF: 0.499 AC: 1734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
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: rs12554686; hg19: chr9-21138433;