rs4867592

Variant names:

• chr5-170220827-C-A
• rs4867592

Your query was ambiguous. Multiple possible variants found:

• chr5-170220827-C-A
• chr5-170220827-C-G
• chr5-170220827-C-T

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 0.447 in 152,076 control chromosomes in the GnomAD database, including 17,628 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 0.45 (17628 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.716 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: 0.447 AC: 67906 AN: 151958 Hom.: 17591 Cov.: 32

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.447 AC: 67975 AN: 152076 Hom.: 17628 Cov.: 32 AF XY: 0.439 AC XY: 32629 AN XY: 74316

African (AFR) AF: 0.723 AC: 30010 AN: 41502

American (AMR) AF: 0.307 AC: 4697 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1120 AN: 3472

East Asian (EAS) AF: 0.116 AC: 600 AN: 5170

South Asian (SAS) AF: 0.247 AC: 1192 AN: 4818

European-Finnish (FIN) AF: 0.377 AC: 3982 AN: 10568

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.368 AC: 25007 AN: 67946

Other (OTH) AF: 0.421 AC: 889 AN: 2114

Alfa AF: 0.402 Hom.: 23603

Bravo AF: 0.454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.39
PhyloP100		0.046

Splicing

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

Other links and lift over

dbSNP: rs4867592; hg19: chr5-169647831;