rs1732778

Variant names:

• chr12-113019120-G-A
• rs1732778

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 0.221 in 151,864 control chromosomes in the GnomAD database, including 4,187 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 0.22 (4187 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 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: 0.222 AC: 33619 AN: 151748 Hom.: 4189 Cov.: 31

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.221 AC: 33628 AN: 151864 Hom.: 4187 Cov.: 31 AF XY: 0.228 AC XY: 16893 AN XY: 74196

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.221

Alfa AF: 0.241 Hom.: 817

Bravo AF: 0.212

Asia WGS AF: 0.371 AC: 1288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.044
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1732778; hg19: chr12-113456925;