chr5-63992792-T-G

Variant names:

• chr5-63992792-T-G
• rs1364041

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 0.144 in 151,802 control chromosomes in the GnomAD database, including 2,282 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 0.14 (2282 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.585
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21805 AN: 151684 Hom.: 2275 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.144 AC: 21826 AN: 151802 Hom.: 2282 Cov.: 32 AF XY: 0.151 AC XY: 11172 AN XY: 74224

African (AFR) AF: 0.107 AC: 4439 AN: 41488

American (AMR) AF: 0.195 AC: 2976 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3466

East Asian (EAS) AF: 0.611 AC: 3147 AN: 5154

South Asian (SAS) AF: 0.176 AC: 849 AN: 4820

European-Finnish (FIN) AF: 0.165 AC: 1752 AN: 10594

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.114 AC: 7752 AN: 67728

Other (OTH) AF: 0.156 AC: 328 AN: 2106

Alfa AF: 0.128 Hom.: 4231

Bravo AF: 0.145

Asia WGS AF: 0.404 AC: 1404 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.7
DANN	Benign	0.82
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs1364041; hg19: chr5-63288619;