rs200113

chr5-8652758-T-C

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 0.137 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

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

Gnomad4 AFR AF: 0.0743

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.152

Alfa AF: 0.149 Hom.: 1747

Bravo AF: 0.129

Asia WGS AF: 0.318 AC: 1104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.32
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs200113; hg19: chr5-8652870;