2-188854236-A-G

Variant names:

• chr2-188854236-A-G
• rs2675399

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 0.23 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.238 AC: 9881 AN: 41438

American (AMR) AF: 0.213 AC: 3246 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1316 AN: 3472

East Asian (EAS) AF: 0.0718 AC: 372 AN: 5184

South Asian (SAS) AF: 0.207 AC: 996 AN: 4820

European-Finnish (FIN) AF: 0.157 AC: 1667 AN: 10588

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16841 AN: 67940

Other (OTH) AF: 0.227 AC: 480 AN: 2114

Alfa AF: 0.247 Hom.: 8620

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
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs2675399; hg19: chr2-189718962;