rs12132178

Positions:

• chr1-100806846-C-A

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 0.477 in 151,950 control chromosomes in the GnomAD database, including 18,099 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 0.48 (18099 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 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: 0.477 AC: 72413 AN: 151832 Hom.: 18092 Cov.: 31

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.477 AC: 72457 AN: 151950 Hom.: 18099 Cov.: 31 AF XY: 0.472 AC XY: 35083 AN XY: 74252

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.493

Alfa AF: 0.536 Hom.: 11025

Bravo AF: 0.467

Asia WGS AF: 0.447 AC: 1554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.7
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12132178; hg19: chr1-101272402;