chr1-159709026-C-T

Variant names:

• chr1-159709026-C-T
• rs2794520

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 0.316 in 151,928 control chromosomes in the GnomAD database, including 8,107 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 0.32 (8107 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 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: 0.316 AC: 48021 AN: 151810 Hom.: 8100 Cov.: 31

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.316 AC: 48046 AN: 151928 Hom.: 8107 Cov.: 31 AF XY: 0.321 AC XY: 23798 AN XY: 74246

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.582

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.333

Alfa AF: 0.334 Hom.: 20390

Bravo AF: 0.312

Asia WGS AF: 0.438 AC: 1522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.61
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2794520; hg19: chr1-159678816;