1-159596857-C-T

Variant names:

• chr1-159596857-C-T
• rs2808636

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.868 in 152,182 control chromosomes in the GnomAD database, including 57,611 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 0.87 (57611 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.705
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 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: 0.868 AC: 131969 AN: 152064 Hom.: 57555 Cov.: 31

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.868 AC: 132086 AN: 152182 Hom.: 57611 Cov.: 31 AF XY: 0.870 AC XY: 64719 AN XY: 74404

African (AFR) AF: 0.938 AC: 38971 AN: 41550

American (AMR) AF: 0.895 AC: 13674 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2631 AN: 3468

East Asian (EAS) AF: 0.986 AC: 5109 AN: 5182

South Asian (SAS) AF: 0.761 AC: 3663 AN: 4816

European-Finnish (FIN) AF: 0.893 AC: 9461 AN: 10596

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.820 AC: 55711 AN: 67968

Other (OTH) AF: 0.861 AC: 1820 AN: 2114

Alfa AF: 0.828 Hom.: 26030

Bravo AF: 0.873

Asia WGS AF: 0.854 AC: 2967 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	0.43
DANN	Benign	0.36
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs2808636; hg19: chr1-159566647;