12-130120384-T-C

Variant names:

• chr12-130120384-T-C
• rs1027557

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 0.27 in 151,984 control chromosomes in the GnomAD database, including 5,955 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 0.27 (5955 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.32
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41041 AN: 151866 Hom.: 5939 Cov.: 33

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.270 AC: 41095 AN: 151984 Hom.: 5955 Cov.: 33 AF XY: 0.273 AC XY: 20253 AN XY: 74288

African (AFR) AF: 0.369 AC: 15315 AN: 41460

American (AMR) AF: 0.196 AC: 2997 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 673 AN: 3472

East Asian (EAS) AF: 0.318 AC: 1625 AN: 5110

South Asian (SAS) AF: 0.271 AC: 1306 AN: 4816

European-Finnish (FIN) AF: 0.293 AC: 3104 AN: 10578

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15205 AN: 67952

Other (OTH) AF: 0.243 AC: 512 AN: 2108

Alfa AF: 0.230 Hom.: 5488

Bravo AF: 0.268

Asia WGS AF: 0.271 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.23
PhyloP100		-4.3

Splicing

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

Other links and lift over

dbSNP: rs1027557; hg19: chr12-130604929;