5-123663261-C-T

Variant names:

• chr5-123663261-C-T
• rs958883

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 0.718 in 151,972 control chromosomes in the GnomAD database, including 39,325 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 0.72 (39325 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.710
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 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: 0.718 AC: 109084 AN: 151854 Hom.: 39292 Cov.: 31

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.718 AC: 109161 AN: 151972 Hom.: 39325 Cov.: 31 AF XY: 0.723 AC XY: 53665 AN XY: 74244

African (AFR) AF: 0.701 AC: 29035 AN: 41412

American (AMR) AF: 0.730 AC: 11146 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2269 AN: 3466

East Asian (EAS) AF: 0.816 AC: 4212 AN: 5164

South Asian (SAS) AF: 0.800 AC: 3863 AN: 4830

European-Finnish (FIN) AF: 0.772 AC: 8136 AN: 10540

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 48072 AN: 67974

Other (OTH) AF: 0.733 AC: 1548 AN: 2112

Alfa AF: 0.703 Hom.: 36546

Bravo AF: 0.715

Asia WGS AF: 0.823 AC: 2862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.82
DANN	Benign	0.20
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs958883; hg19: chr5-122998955;