rs4866484

Variant names:

• chr5-2417911-A-G
• rs4866484

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 0.279 in 152,158 control chromosomes in the GnomAD database, including 6,094 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 0.28 (6094 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.84
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.368 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: 0.279 AC: 42433 AN: 152038 Hom.: 6088 Cov.: 33

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.279 AC: 42456 AN: 152158 Hom.: 6094 Cov.: 33 AF XY: 0.282 AC XY: 20955 AN XY: 74408

African (AFR) AF: 0.296 AC: 12296 AN: 41516

American (AMR) AF: 0.243 AC: 3714 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1023 AN: 3464

East Asian (EAS) AF: 0.287 AC: 1485 AN: 5168

South Asian (SAS) AF: 0.382 AC: 1842 AN: 4816

European-Finnish (FIN) AF: 0.285 AC: 3025 AN: 10602

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18312 AN: 67986

Other (OTH) AF: 0.258 AC: 544 AN: 2112

Alfa AF: 0.271 Hom.: 9887

Bravo AF: 0.270

Asia WGS AF: 0.327 AC: 1132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.16
DANN	Benign	0.19
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs4866484; hg19: chr5-2418025;