5-18028563-A-T

Variant names:

• chr5-18028563-A-T
• rs6880596

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 0.182 in 152,138 control chromosomes in the GnomAD database, including 3,517 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 0.18 (3517 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.762
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.345 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: 0.182 AC: 27658 AN: 152020 Hom.: 3495 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0888

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0986

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.182 AC: 27726 AN: 152138 Hom.: 3517 Cov.: 32 AF XY: 0.180 AC XY: 13390 AN XY: 74374

African (AFR) AF: 0.350 AC: 14522 AN: 41472

American (AMR) AF: 0.192 AC: 2933 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0660 AC: 229 AN: 3468

East Asian (EAS) AF: 0.232 AC: 1202 AN: 5178

South Asian (SAS) AF: 0.156 AC: 754 AN: 4826

European-Finnish (FIN) AF: 0.0888 AC: 940 AN: 10588

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0986 AC: 6705 AN: 68004

Other (OTH) AF: 0.155 AC: 327 AN: 2114

Alfa AF: 0.0669 Hom.: 89

Bravo AF: 0.197

Asia WGS AF: 0.210 AC: 730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.025
DANN	Benign	0.24
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs6880596; hg19: chr5-18028672;