rs12545648

Variant names:

• chr8-127522510-C-T
• rs12545648

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 0.908 in 152,262 control chromosomes in the GnomAD database, including 62,869 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 0.91 (62869 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.933 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: 0.908 AC: 138167 AN: 152144 Hom.: 62822 Cov.: 33

Gnomad AFR AF: 0.941

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.927

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.908 AC: 138270 AN: 152262 Hom.: 62869 Cov.: 33 AF XY: 0.906 AC XY: 67434 AN XY: 74446

Gnomad4 AFR AF: 0.941

Gnomad4 AMR AF: 0.927

Gnomad4 ASJ AF: 0.938

Gnomad4 EAS AF: 0.855

Gnomad4 SAS AF: 0.870

Gnomad4 FIN AF: 0.839

Gnomad4 NFE AF: 0.899

Gnomad4 OTH AF: 0.914

Alfa AF: 0.899 Hom.: 14636

Bravo AF: 0.915

Asia WGS AF: 0.827 AC: 2878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12545648; hg19: chr8-128534755;