rs4657393

Variant names:

• chr1-165043174-C-T
• rs4657393

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 0.401 in 151,978 control chromosomes in the GnomAD database, including 12,733 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 0.40 (12733 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.829
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.542 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: 0.401 AC: 60874 AN: 151860 Hom.: 12713 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.401 AC: 60943 AN: 151978 Hom.: 12733 Cov.: 32 AF XY: 0.406 AC XY: 30184 AN XY: 74272

African (AFR) AF: 0.376 AC: 15578 AN: 41478

American (AMR) AF: 0.552 AC: 8428 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1529 AN: 3470

East Asian (EAS) AF: 0.525 AC: 2709 AN: 5162

South Asian (SAS) AF: 0.544 AC: 2614 AN: 4804

European-Finnish (FIN) AF: 0.342 AC: 3599 AN: 10528

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25201 AN: 67938

Other (OTH) AF: 0.418 AC: 885 AN: 2116

Alfa AF: 0.377 Hom.: 1375

Bravo AF: 0.416

Asia WGS AF: 0.549 AC: 1908 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	13
DANN	Benign	0.66
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs4657393; hg19: chr1-165012411;