rs12545648

Positions:

• chr8-127522510-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;