rs4920821

Variant names:

• chr5-85142786-G-A
• rs4920821

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 0.532 in 151,800 control chromosomes in the GnomAD database, including 21,878 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 0.53 (21878 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752
• Publications: 0 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 (AFR) allele frequency at 95% confidence interval = 0.62 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: 0.532 AC: 80720 AN: 151682 Hom.: 21841 Cov.: 31

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.532 AC: 80814 AN: 151800 Hom.: 21878 Cov.: 31 AF XY: 0.532 AC XY: 39481 AN XY: 74174

African (AFR) AF: 0.627 AC: 25936 AN: 41392

American (AMR) AF: 0.535 AC: 8162 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1493 AN: 3470

East Asian (EAS) AF: 0.607 AC: 3110 AN: 5120

South Asian (SAS) AF: 0.534 AC: 2572 AN: 4816

European-Finnish (FIN) AF: 0.479 AC: 5041 AN: 10532

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32917 AN: 67908

Other (OTH) AF: 0.509 AC: 1074 AN: 2112

Alfa AF: 0.499 Hom.: 10016

Bravo AF: 0.543

Asia WGS AF: 0.560 AC: 1948 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	1.3
DANN	Benign	0.40
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs4920821; hg19: chr5-84438604; COSMIC: COSV60163411;