rs1559033

chr2-15744432-C-T

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 0.0444 in 285,326 control chromosomes in the GnomAD database, including 1,172 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 0.069 (1050 hom., cov: 32)
  • Exomes 𝑓: 0.016 (122 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0691 AC: 10509 AN: 151998 Hom.: 1042 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0391

Gnomad ASJ AF: 0.0469

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00270

Gnomad FIN AF: 0.00774

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00898

Gnomad OTH AF: 0.0588

GnomAD4 exome AF: 0.0159 AC: 2117 AN: 133210 Hom.: 122 AF XY: 0.0140 AC XY: 1036 AN XY: 73864

Gnomad4 AFR exome AF: 0.218

Gnomad4 AMR exome AF: 0.0210

Gnomad4 ASJ exome AF: 0.0366

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00250

Gnomad4 FIN exome AF: 0.00776

Gnomad4 NFE exome AF: 0.00780

Gnomad4 OTH exome AF: 0.0201

GnomAD4 genome AF: 0.0693 AC: 10548 AN: 152116 Hom.: 1050 Cov.: 32 AF XY: 0.0675 AC XY: 5019 AN XY: 74368

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.0390

Gnomad4 ASJ AF: 0.0469

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00249

Gnomad4 FIN AF: 0.00774

Gnomad4 NFE AF: 0.00899

Gnomad4 OTH AF: 0.0582

Alfa AF: 0.0423 Hom.: 65

Bravo AF: 0.0775

Asia WGS AF: 0.0230 AC: 82 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.15
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1559033; hg19: chr2-15884556;