rs2494251

chr1-159311361-G-Achr1-159311361-G-Cchr1-159311361-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;