chr1-203468576-T-C

Variant names:

• chr1-203468576-T-C
• rs2794452

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 0.427 in 152,070 control chromosomes in the GnomAD database, including 14,288 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 0.43 (14288 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.81
• Publications: 5 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 = 0.565 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64802 AN: 151952 Hom.: 14274 Cov.: 32

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.427 AC: 64871 AN: 152070 Hom.: 14288 Cov.: 32 AF XY: 0.430 AC XY: 31950 AN XY: 74320

African (AFR) AF: 0.514 AC: 21300 AN: 41476

American (AMR) AF: 0.493 AC: 7530 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1089 AN: 3466

East Asian (EAS) AF: 0.582 AC: 3008 AN: 5168

South Asian (SAS) AF: 0.423 AC: 2038 AN: 4820

European-Finnish (FIN) AF: 0.350 AC: 3701 AN: 10562

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24905 AN: 67984

Other (OTH) AF: 0.402 AC: 849 AN: 2110

Alfa AF: 0.339 Hom.: 1635

Bravo AF: 0.441

Asia WGS AF: 0.511 AC: 1778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.017
DANN	Benign	0.28
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs2794452; hg19: chr1-203437704;