5-8652758-T-C

Variant names:

• chr5-8652758-T-C
• rs200113

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 0.137 in 152,022 control chromosomes in the GnomAD database, including 1,676 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 (1676 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.305 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: 0.137 AC: 20855 AN: 151904 Hom.: 1676 Cov.: 31

Gnomad AFR AF: 0.0745

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.137 AC: 20856 AN: 152022 Hom.: 1676 Cov.: 31 AF XY: 0.141 AC XY: 10463 AN XY: 74286

African (AFR) AF: 0.0743 AC: 3085 AN: 41498

American (AMR) AF: 0.133 AC: 2033 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 687 AN: 3466

East Asian (EAS) AF: 0.214 AC: 1105 AN: 5152

South Asian (SAS) AF: 0.318 AC: 1531 AN: 4808

European-Finnish (FIN) AF: 0.169 AC: 1783 AN: 10550

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10138 AN: 67966

Other (OTH) AF: 0.152 AC: 320 AN: 2112

Alfa AF: 0.146 Hom.: 4775

Bravo AF: 0.129

Asia WGS AF: 0.318 AC: 1104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
DANN	Benign	0.64
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs200113; hg19: chr5-8652870;