1-159665231-C-T

Variant names:

• chr1-159665231-C-T
• rs2794500

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 0.436 in 151,944 control chromosomes in the GnomAD database, including 16,149 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 0.44 (16149 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 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: 0.435 AC: 66111 AN: 151826 Hom.: 16127 Cov.: 31

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.436 AC: 66185 AN: 151944 Hom.: 16149 Cov.: 31 AF XY: 0.430 AC XY: 31962 AN XY: 74244

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.416

Alfa AF: 0.376 Hom.: 6717

Bravo AF: 0.439

Asia WGS AF: 0.227 AC: 791 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	3.3
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2794500; hg19: chr1-159635021;