rs1732778

Variant names:

• chr12-113019120-G-A
• rs1732778

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 0.221 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
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.124 AC: 5143 AN: 41460

American (AMR) AF: 0.232 AC: 3533 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3472

East Asian (EAS) AF: 0.475 AC: 2445 AN: 5150

South Asian (SAS) AF: 0.327 AC: 1570 AN: 4804

European-Finnish (FIN) AF: 0.318 AC: 3353 AN: 10534

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16450 AN: 67884

Other (OTH) AF: 0.221 AC: 465 AN: 2106

Alfa AF: 0.238 Hom.: 823

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
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs1732778; hg19: chr12-113456925;