chr1-228466494-C-T

Variant names:

• chr1-228466494-C-T
• rs4653963

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 0.197 in 150,598 control chromosomes in the GnomAD database, including 8,163 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 0.20 (8163 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.617 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: 0.196 AC: 29515 AN: 150482 Hom.: 8135 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0645

Gnomad EAS AF: 0.0761

Gnomad SAS AF: 0.0214

Gnomad FIN AF: 0.0102

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0172

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.197 AC: 29596 AN: 150598 Hom.: 8163 Cov.: 32 AF XY: 0.192 AC XY: 14104 AN XY: 73562

African (AFR) AF: 0.624 AC: 25150 AN: 40314

American (AMR) AF: 0.136 AC: 2066 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.0645 AC: 223 AN: 3460

East Asian (EAS) AF: 0.0765 AC: 392 AN: 5124

South Asian (SAS) AF: 0.0208 AC: 100 AN: 4800

European-Finnish (FIN) AF: 0.0102 AC: 107 AN: 10522

Middle Eastern (MID) AF: 0.101 AC: 29 AN: 286

European-Non Finnish (NFE) AF: 0.0172 AC: 1165 AN: 67912

Other (OTH) AF: 0.155 AC: 324 AN: 2092

Alfa AF: 0.0496 Hom.: 196

Bravo AF: 0.233

Asia WGS AF: 0.0800 AC: 270 AN: 3404

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.25
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs4653963; hg19: chr1-228654195;