5-28340066-G-A

Variant names:

• chr5-28340066-G-A
• rs11949289

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 0.402 in 151,826 control chromosomes in the GnomAD database, including 13,823 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 0.40 (13823 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.52 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: 0.402 AC: 61012 AN: 151708 Hom.: 13821 Cov.: 31

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.0776

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.402 AC: 61032 AN: 151826 Hom.: 13823 Cov.: 31 AF XY: 0.396 AC XY: 29397 AN XY: 74184

African (AFR) AF: 0.242 AC: 10018 AN: 41420

American (AMR) AF: 0.354 AC: 5388 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1408 AN: 3462

East Asian (EAS) AF: 0.0778 AC: 400 AN: 5142

South Asian (SAS) AF: 0.333 AC: 1603 AN: 4810

European-Finnish (FIN) AF: 0.478 AC: 5042 AN: 10554

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.525 AC: 35659 AN: 67914

Other (OTH) AF: 0.420 AC: 885 AN: 2108

Alfa AF: 0.477 Hom.: 59982

Bravo AF: 0.383

Asia WGS AF: 0.196 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.43
PhyloP100		-0.027

Splicing

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

Other links and lift over

dbSNP: rs11949289; hg19: chr5-28340173;