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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.335 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

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.363

Alfa AF: 0.385 Hom.: 5794

Bravo AF: 0.318

Asia WGS AF: 0.237 AC: 824 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2494251; hg19: chr1-159281151;