chr5-5511877-G-A

Variant names:

• chr5-5511877-G-A
• rs252928

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 0.427 in 152,086 control chromosomes in the GnomAD database, including 14,739 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 0.43 (14739 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 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: 0.427 AC: 64852 AN: 151968 Hom.: 14711 Cov.: 33

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.427 AC: 64931 AN: 152086 Hom.: 14739 Cov.: 33 AF XY: 0.430 AC XY: 31983 AN XY: 74340

African (AFR) AF: 0.561 AC: 23289 AN: 41494

American (AMR) AF: 0.362 AC: 5537 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1176 AN: 3472

East Asian (EAS) AF: 0.674 AC: 3474 AN: 5158

South Asian (SAS) AF: 0.375 AC: 1804 AN: 4808

European-Finnish (FIN) AF: 0.446 AC: 4720 AN: 10576

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23753 AN: 67978

Other (OTH) AF: 0.380 AC: 804 AN: 2116

Alfa AF: 0.337 Hom.: 4749

Bravo AF: 0.425

Asia WGS AF: 0.509 AC: 1769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.074
DANN	Benign	0.35
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs252928; hg19: chr5-5511990;