5-63522073-G-A

Variant names:

• chr5-63522073-G-A
• rs255414

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 0.769 in 151,928 control chromosomes in the GnomAD database, including 45,534 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 0.77 (45534 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.769 AC: 116761 AN: 151810 Hom.: 45496 Cov.: 33

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.769 AC: 116858 AN: 151928 Hom.: 45534 Cov.: 33 AF XY: 0.776 AC XY: 57644 AN XY: 74250

African (AFR) AF: 0.650 AC: 26900 AN: 41412

American (AMR) AF: 0.813 AC: 12389 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.797 AC: 2768 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5144 AN: 5156

South Asian (SAS) AF: 0.851 AC: 4109 AN: 4830

European-Finnish (FIN) AF: 0.854 AC: 9038 AN: 10588

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54018 AN: 67918

Other (OTH) AF: 0.757 AC: 1597 AN: 2110

Alfa AF: 0.788 Hom.: 88399

Bravo AF: 0.760

Asia WGS AF: 0.906 AC: 3118 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.90
DANN	Benign	0.34
PhyloP100		0.079

Splicing

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

Other links and lift over

dbSNP: rs255414; hg19: chr5-62817900;