rs1443512

chr12-53948900-A-Cchr12-53948900-A-Gchr12-53948900-A-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 0.666 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.666 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

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.821

Gnomad4 SAS AF: 0.691

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.769

Gnomad4 OTH AF: 0.696

Alfa AF: 0.751 Hom.: 86517

Bravo AF: 0.660

Asia WGS AF: 0.780 AC: 2711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.2
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1443512; hg19: chr12-54342684;