rs2284136

Variant names:

• chr12-5042832-C-T
• rs2284136

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 0.401 in 152,018 control chromosomes in the GnomAD database, including 12,638 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 0.40 (12638 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 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: 0.401 AC: 60903 AN: 151900 Hom.: 12619 Cov.: 32

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.416

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.401 AC: 60976 AN: 152018 Hom.: 12638 Cov.: 32 AF XY: 0.406 AC XY: 30199 AN XY: 74318

African (AFR) AF: 0.483 AC: 20023 AN: 41448

American (AMR) AF: 0.333 AC: 5096 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1579 AN: 3468

East Asian (EAS) AF: 0.499 AC: 2579 AN: 5170

South Asian (SAS) AF: 0.491 AC: 2364 AN: 4818

European-Finnish (FIN) AF: 0.416 AC: 4388 AN: 10560

Middle Eastern (MID) AF: 0.410 AC: 118 AN: 288

European-Non Finnish (NFE) AF: 0.349 AC: 23730 AN: 67960

Other (OTH) AF: 0.380 AC: 804 AN: 2116

Alfa AF: 0.366 Hom.: 28878

Bravo AF: 0.393

Asia WGS AF: 0.525 AC: 1824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
DANN	Benign	0.47
PhyloP100		0.047

Splicing

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

Other links and lift over

dbSNP: rs2284136; hg19: chr12-5151998;