rs289838

Variant names:

• chr2-151266887-G-A
• rs289838

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 0.245 in 152,096 control chromosomes in the GnomAD database, including 6,927 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 0.25 (6927 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 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: 0.245 AC: 37230 AN: 151978 Hom.: 6914 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.0712

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.245 AC: 37289 AN: 152096 Hom.: 6927 Cov.: 32 AF XY: 0.240 AC XY: 17818 AN XY: 74374

African (AFR) AF: 0.527 AC: 21863 AN: 41456

American (AMR) AF: 0.160 AC: 2448 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 597 AN: 3472

East Asian (EAS) AF: 0.125 AC: 645 AN: 5158

South Asian (SAS) AF: 0.232 AC: 1118 AN: 4814

European-Finnish (FIN) AF: 0.0712 AC: 754 AN: 10596

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9270 AN: 68008

Other (OTH) AF: 0.219 AC: 461 AN: 2108

Alfa AF: 0.163 Hom.: 1473

Bravo AF: 0.260

Asia WGS AF: 0.206 AC: 715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.25
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs289838; hg19: chr2-152123401;