2-185259982-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 0.293 in 151,838 control chromosomes in the GnomAD database, including 7,616 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 0.29 (7616 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.385 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: 0.294 AC: 44575 AN: 151722 Hom.: 7617 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.293 AC: 44564 AN: 151838 Hom.: 7616 Cov.: 32 AF XY: 0.292 AC XY: 21655 AN XY: 74192

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.292

Alfa AF: 0.332 Hom.: 3750

Bravo AF: 0.287

Asia WGS AF: 0.215 AC: 749 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.62
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: rs1559510; hg19: chr2-186124709;