rs4655058

Variant names:

• chr1-22402068-C-T
• rs4655058

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 0.264 in 151,750 control chromosomes in the GnomAD database, including 5,507 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 0.26 (5507 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40090 AN: 151632 Hom.: 5506 Cov.: 31

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.264 AC: 40092 AN: 151750 Hom.: 5507 Cov.: 31 AF XY: 0.267 AC XY: 19812 AN XY: 74140

African (AFR) AF: 0.189 AC: 7808 AN: 41388

American (AMR) AF: 0.282 AC: 4299 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1109 AN: 3470

East Asian (EAS) AF: 0.184 AC: 948 AN: 5158

South Asian (SAS) AF: 0.310 AC: 1487 AN: 4796

European-Finnish (FIN) AF: 0.323 AC: 3381 AN: 10476

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20078 AN: 67912

Other (OTH) AF: 0.262 AC: 554 AN: 2116

Alfa AF: 0.279 Hom.: 786

Bravo AF: 0.255

Asia WGS AF: 0.284 AC: 986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.0
DANN	Benign	0.89
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs4655058; hg19: chr1-22728561;