chr5-63522073-G-A

Position:

• chr5-63522073-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.813

Gnomad4 ASJ AF: 0.797

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.851

Gnomad4 FIN AF: 0.854

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.757

Alfa AF: 0.799 Hom.: 59304

Bravo AF: 0.760

Asia WGS AF: 0.906 AC: 3118 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs255414; hg19: chr5-62817900;