rs12544183

Variant names:

• chr8-92286476-G-T
• rs12544183

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 0.0652 in 152,176 control chromosomes in the GnomAD database, including 454 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 0.065 (454 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0999 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: 0.0653 AC: 9927 AN: 152058 Hom.: 454 Cov.: 32

Gnomad AFR AF: 0.0156

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.0737

Gnomad ASJ AF: 0.0334

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0831

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0937

Gnomad OTH AF: 0.0540

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

GnomAD4 genome AF: 0.0652 AC: 9924 AN: 152176 Hom.: 454 Cov.: 32 AF XY: 0.0641 AC XY: 4771 AN XY: 74394

African (AFR) AF: 0.0155 AC: 645 AN: 41546

American (AMR) AF: 0.0737 AC: 1124 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0334 AC: 116 AN: 3470

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5168

South Asian (SAS) AF: 0.108 AC: 519 AN: 4824

European-Finnish (FIN) AF: 0.0831 AC: 882 AN: 10608

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0937 AC: 6368 AN: 67986

Other (OTH) AF: 0.0535 AC: 113 AN: 2114

Alfa AF: 0.0776 Hom.: 107

Bravo AF: 0.0625

Asia WGS AF: 0.0420 AC: 146 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.47
DANN	Benign	0.30
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs12544183; hg19: chr8-93298704;