rs12549576

Variant names:

• chr8-111963912-A-G
• rs12549576

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 0.0411 in 152,168 control chromosomes in the GnomAD database, including 196 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 0.041 (196 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.294

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.129 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: 0.0411 AC: 6244 AN: 152050 Hom.: 193 Cov.: 32

Gnomad AFR AF: 0.0493

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0866

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.0739

Gnomad FIN AF: 0.0232

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0212

Gnomad OTH AF: 0.0394

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

GnomAD4 genome AF: 0.0411 AC: 6253 AN: 152168 Hom.: 196 Cov.: 32 AF XY: 0.0433 AC XY: 3224 AN XY: 74390

Gnomad4 AFR AF: 0.0494

Gnomad4 AMR AF: 0.0867

Gnomad4 ASJ AF: 0.00807

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.0737

Gnomad4 FIN AF: 0.0232

Gnomad4 NFE AF: 0.0212

Gnomad4 OTH AF: 0.0394

Alfa AF: 0.0269 Hom.: 91

Bravo AF: 0.0452

Asia WGS AF: 0.103 AC: 357 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.0
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12549576; hg19: chr8-112976141;