rs2794521

Variant names:

• chr1-159715306-C-T
• rs2794521

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 0.775 in 149,672 control chromosomes in the GnomAD database, including 45,152 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 0.77 (45152 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 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: 0.775 AC: 115874 AN: 149554 Hom.: 45101 Cov.: 23

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.775 AC: 115985 AN: 149672 Hom.: 45152 Cov.: 23 AF XY: 0.777 AC XY: 56704 AN XY: 72934

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.802

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.780

Alfa AF: 0.734 Hom.: 34101

Bravo AF: 0.779

Asia WGS AF: 0.739 AC: 2573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2794521; hg19: chr1-159685096;