12-53948900-A-C

Variant names:

• chr12-53948900-A-C
• rs1443512

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 0.666 in 152,000 control chromosomes in the GnomAD database, including 35,466 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 0.67 (35466 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.256
• Publications: 87 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.801 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101194 AN: 151882 Hom.: 35456 Cov.: 31

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.666 AC: 101241 AN: 152000 Hom.: 35466 Cov.: 31 AF XY: 0.666 AC XY: 49491 AN XY: 74324

African (AFR) AF: 0.424 AC: 17574 AN: 41400

American (AMR) AF: 0.749 AC: 11433 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2381 AN: 3470

East Asian (EAS) AF: 0.821 AC: 4242 AN: 5166

South Asian (SAS) AF: 0.691 AC: 3321 AN: 4804

European-Finnish (FIN) AF: 0.721 AC: 7634 AN: 10592

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.769 AC: 52287 AN: 67980

Other (OTH) AF: 0.696 AC: 1469 AN: 2110

Alfa AF: 0.740 Hom.: 181485

Bravo AF: 0.660

Asia WGS AF: 0.780 AC: 2711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.2
DANN	Benign	0.56
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs1443512; hg19: chr12-54342684;