2-188854236-A-G

Variant names:

• chr2-188854236-A-G
• rs2675399

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 0.23 in 152,028 control chromosomes in the GnomAD database, including 4,215 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 0.23 (4215 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.245 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: 0.230 AC: 34894 AN: 151910 Hom.: 4200 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.0716

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.230 AC: 34942 AN: 152028 Hom.: 4215 Cov.: 32 AF XY: 0.225 AC XY: 16731 AN XY: 74304

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.0718

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.227

Alfa AF: 0.248 Hom.: 2715

Bravo AF: 0.233

Asia WGS AF: 0.160 AC: 560 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.46
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: rs2675399; hg19: chr2-189718962;