2-198786880-A-G

Position:

• chr2-198786880-A-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 0.293 in 152,024 control chromosomes in the GnomAD database, including 8,025 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 (8025 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

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 (EAS) allele frequency at 95% confidence interval = 0.536 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: 0.293 AC: 44473 AN: 151906 Hom.: 8019 Cov.: 32

Gnomad AFR AF: 0.0779

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.293 AC: 44483 AN: 152024 Hom.: 8025 Cov.: 32 AF XY: 0.296 AC XY: 22016 AN XY: 74286

Gnomad4 AFR AF: 0.0778

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.321

Alfa AF: 0.339 Hom.: 2127

Bravo AF: 0.288

Asia WGS AF: 0.490 AC: 1704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.052
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332426; hg19: chr2-199651604;