rs4920520

Variant names:

• chr1-18603348-G-A
• rs4920520

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 0.466 in 151,840 control chromosomes in the GnomAD database, including 16,852 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 0.47 (16852 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.44
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70677 AN: 151720 Hom.: 16825 Cov.: 31

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.466 AC: 70756 AN: 151840 Hom.: 16852 Cov.: 31 AF XY: 0.465 AC XY: 34530 AN XY: 74182

African (AFR) AF: 0.496 AC: 20533 AN: 41360

American (AMR) AF: 0.426 AC: 6499 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1458 AN: 3466

East Asian (EAS) AF: 0.144 AC: 745 AN: 5168

South Asian (SAS) AF: 0.387 AC: 1861 AN: 4808

European-Finnish (FIN) AF: 0.545 AC: 5746 AN: 10538

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32510 AN: 67928

Other (OTH) AF: 0.464 AC: 979 AN: 2110

Alfa AF: 0.468 Hom.: 33604

Bravo AF: 0.453

Asia WGS AF: 0.262 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	13
DANN	Benign	0.32
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs4920520; hg19: chr1-18929842;