rs12549576

Positions:

• chr8-111963912-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;