rs2352267

chr2-189584239-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 0.409 in 152,044 control chromosomes in the GnomAD database, including 13,155 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 0.41 (13155 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 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: 0.409 AC: 62097 AN: 151926 Hom.: 13140 Cov.: 32

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.409 AC: 62141 AN: 152044 Hom.: 13155 Cov.: 32 AF XY: 0.403 AC XY: 29966 AN XY: 74308

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.387

Alfa AF: 0.402 Hom.: 16546

Bravo AF: 0.404

Asia WGS AF: 0.262 AC: 913 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	11
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2352267; hg19: chr2-190448965;