rs6873793

chr5-3092078-C-T

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 0.558 in 152,042 control chromosomes in the GnomAD database, including 24,437 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 0.56 (24437 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.637 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: 0.558 AC: 84737 AN: 151924 Hom.: 24401 Cov.: 33

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.558 AC: 84834 AN: 152042 Hom.: 24437 Cov.: 33 AF XY: 0.549 AC XY: 40829 AN XY: 74308

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.568

Alfa AF: 0.559 Hom.: 38051

Bravo AF: 0.569

Asia WGS AF: 0.321 AC: 1119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.8
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6873793; hg19: chr5-3092192;