rs2352267

Variant names:

• chr2-189584239-A-G
• rs2352267

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 0.409 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
• Publications: 7 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.488 AC: 20206 AN: 41446

American (AMR) AF: 0.294 AC: 4497 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1123 AN: 3470

East Asian (EAS) AF: 0.186 AC: 965 AN: 5188

South Asian (SAS) AF: 0.386 AC: 1864 AN: 4830

European-Finnish (FIN) AF: 0.374 AC: 3940 AN: 10548

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28178 AN: 67970

Other (OTH) AF: 0.387 AC: 816 AN: 2108

Alfa AF: 0.403 Hom.: 20851

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
PhyloP100		0.25
PromoterAI		0.0026	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2352267; hg19: chr2-190448965;