rs12132178

Variant names:

• chr1-100806846-C-A
• rs12132178

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 0.477 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.343 AC: 14217 AN: 41422

American (AMR) AF: 0.458 AC: 7004 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2207 AN: 3472

East Asian (EAS) AF: 0.388 AC: 2007 AN: 5170

South Asian (SAS) AF: 0.539 AC: 2587 AN: 4804

European-Finnish (FIN) AF: 0.438 AC: 4614 AN: 10546

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 37993 AN: 67940

Other (OTH) AF: 0.493 AC: 1042 AN: 2112

Alfa AF: 0.537 Hom.: 12286

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
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs12132178; hg19: chr1-101272402;