chr2-198786880-A-G

Variant names:

• chr2-198786880-A-G
• rs9332426

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 0.293 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0778 AC: 3232 AN: 41518

American (AMR) AF: 0.347 AC: 5295 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1493 AN: 3466

East Asian (EAS) AF: 0.553 AC: 2849 AN: 5154

South Asian (SAS) AF: 0.533 AC: 2566 AN: 4814

European-Finnish (FIN) AF: 0.296 AC: 3128 AN: 10572

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24838 AN: 67950

Other (OTH) AF: 0.321 AC: 677 AN: 2106

Alfa AF: 0.351 Hom.: 4192

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
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs9332426; hg19: chr2-199651604;