5-80595228-G-A

Variant names:

• chr5-80595228-G-A
• rs6883095

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 0.459 in 152,048 control chromosomes in the GnomAD database, including 18,327 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 0.46 (18327 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69837 AN: 151930 Hom.: 18325 Cov.: 31

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.459 AC: 69852 AN: 152048 Hom.: 18327 Cov.: 31 AF XY: 0.464 AC XY: 34525 AN XY: 74342

African (AFR) AF: 0.209 AC: 8681 AN: 41478

American (AMR) AF: 0.594 AC: 9068 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1890 AN: 3468

East Asian (EAS) AF: 0.886 AC: 4586 AN: 5178

South Asian (SAS) AF: 0.411 AC: 1979 AN: 4816

European-Finnish (FIN) AF: 0.592 AC: 6261 AN: 10576

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35772 AN: 67964

Other (OTH) AF: 0.471 AC: 993 AN: 2108

Alfa AF: 0.494 Hom.: 10996

Bravo AF: 0.458

Asia WGS AF: 0.608 AC: 2111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.7
DANN	Benign	0.59
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs6883095; hg19: chr5-79891047;