chr2-59093319-C-G

Position:

• chr2-59093319-C-G

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 0.452 in 152,064 control chromosomes in the GnomAD database, including 16,953 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 0.45 (16953 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68723 AN: 151946 Hom.: 16928 Cov.: 32

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.452 AC: 68805 AN: 152064 Hom.: 16953 Cov.: 32 AF XY: 0.451 AC XY: 33504 AN XY: 74326

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.408

Alfa AF: 0.412 Hom.: 1893

Bravo AF: 0.465

Asia WGS AF: 0.379 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.075
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10211390; hg19: chr2-59320454;