rs2794521

chr1-159715306-C-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 0.775 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/exons	MANE	UniProt

Ensembl

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