5-63955464-A-G

Variant names:

• chr5-63955464-A-G
• rs72767932

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 0.109 in 152,068 control chromosomes in the GnomAD database, including 1,051 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 0.11 (1051 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16591 AN: 151950 Hom.: 1049 Cov.: 32

Gnomad AFR AF: 0.0876

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.0717

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.109 AC: 16586 AN: 152068 Hom.: 1051 Cov.: 32 AF XY: 0.107 AC XY: 7984 AN XY: 74330

African (AFR) AF: 0.0873 AC: 3623 AN: 41478

American (AMR) AF: 0.126 AC: 1917 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 563 AN: 3472

East Asian (EAS) AF: 0.00213 AC: 11 AN: 5166

South Asian (SAS) AF: 0.176 AC: 845 AN: 4804

European-Finnish (FIN) AF: 0.0717 AC: 759 AN: 10590

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8353 AN: 67982

Other (OTH) AF: 0.103 AC: 218 AN: 2108

Alfa AF: 0.115 Hom.: 144

Bravo AF: 0.110

Asia WGS AF: 0.0800 AC: 280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.7
DANN	Benign	0.75
PhyloP100		0.081

Splicing

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

Other links and lift over

dbSNP: rs72767932; hg19: chr5-63251291;