rs12545648

Variant names:

• chr8-127522510-C-T
• rs12545648

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 0.908 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.941 AC: 39114 AN: 41558

American (AMR) AF: 0.927 AC: 14185 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.938 AC: 3254 AN: 3470

East Asian (EAS) AF: 0.855 AC: 4428 AN: 5180

South Asian (SAS) AF: 0.870 AC: 4194 AN: 4820

European-Finnish (FIN) AF: 0.839 AC: 8880 AN: 10584

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.899 AC: 61173 AN: 68028

Other (OTH) AF: 0.914 AC: 1934 AN: 2116

Alfa AF: 0.900 Hom.: 35634

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
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs12545648; hg19: chr8-128534755;