rs1732778

Positions:

• chr12-113019120-G-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 0.221 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;