rs1867898

Variant names:

• chr2-133762000-G-A
• rs1867898

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 0.221 in 152,042 control chromosomes in the GnomAD database, including 3,968 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 0.22 (3968 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 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: 0.221 AC: 33619 AN: 151924 Hom.: 3960 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.221 AC: 33644 AN: 152042 Hom.: 3968 Cov.: 32 AF XY: 0.225 AC XY: 16715 AN XY: 74314

African (AFR) AF: 0.256 AC: 10620 AN: 41468

American (AMR) AF: 0.156 AC: 2378 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 773 AN: 3472

East Asian (EAS) AF: 0.365 AC: 1878 AN: 5148

South Asian (SAS) AF: 0.289 AC: 1392 AN: 4812

European-Finnish (FIN) AF: 0.219 AC: 2322 AN: 10580

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.199 AC: 13556 AN: 67980

Other (OTH) AF: 0.215 AC: 453 AN: 2108

Alfa AF: 0.229 Hom.: 553

Bravo AF: 0.216

Asia WGS AF: 0.275 AC: 956 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.58
DANN	Benign	0.60
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1867898; hg19: chr2-134519571;