5-99833655-C-T

Variant names:

• chr5-99833655-C-T
• rs6888673

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 0.737 in 151,684 control chromosomes in the GnomAD database, including 41,373 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 0.74 (41373 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 3 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 = 0.822 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111611 AN: 151566 Hom.: 41327 Cov.: 30

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.737 AC: 111716 AN: 151684 Hom.: 41373 Cov.: 30 AF XY: 0.737 AC XY: 54626 AN XY: 74124

African (AFR) AF: 0.830 AC: 34366 AN: 41414

American (AMR) AF: 0.721 AC: 10974 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2832 AN: 3468

East Asian (EAS) AF: 0.640 AC: 3277 AN: 5118

South Asian (SAS) AF: 0.726 AC: 3503 AN: 4828

European-Finnish (FIN) AF: 0.710 AC: 7487 AN: 10538

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.692 AC: 46897 AN: 67794

Other (OTH) AF: 0.742 AC: 1556 AN: 2096

Alfa AF: 0.714 Hom.: 9874

Bravo AF: 0.742

Asia WGS AF: 0.711 AC: 2474 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	0.89
DANN	Benign	0.70
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs6888673; hg19: chr5-99169359;