rs2494251

Variant names:

• chr1-159311361-G-A
• rs2494251

Your query was ambiguous. Multiple possible variants found:

• chr1-159311361-G-A
• chr1-159311361-G-C
• chr1-159311361-G-T

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 0.334 in 152,038 control chromosomes in the GnomAD database, including 10,182 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 0.33 (10182 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771
• Publications: 10 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 (NFE) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50832 AN: 151920 Hom.: 10185 Cov.: 33

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.334 AC: 50843 AN: 152038 Hom.: 10182 Cov.: 33 AF XY: 0.331 AC XY: 24625 AN XY: 74324

African (AFR) AF: 0.116 AC: 4810 AN: 41488

American (AMR) AF: 0.347 AC: 5293 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1204 AN: 3472

East Asian (EAS) AF: 0.264 AC: 1365 AN: 5166

South Asian (SAS) AF: 0.293 AC: 1413 AN: 4824

European-Finnish (FIN) AF: 0.438 AC: 4628 AN: 10556

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30900 AN: 67952

Other (OTH) AF: 0.363 AC: 766 AN: 2112

Alfa AF: 0.389 Hom.: 6502

Bravo AF: 0.318

Asia WGS AF: 0.237 AC: 824 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.6
DANN	Benign	0.71
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs2494251; hg19: chr1-159281151;