rs6450023

Positions:

• chr5-69230236-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 0.326 in 151,956 control chromosomes in the GnomAD database, including 10,341 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 0.33 (10341 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 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: 0.325 AC: 49401 AN: 151838 Hom.: 10308 Cov.: 31

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.326 AC: 49482 AN: 151956 Hom.: 10341 Cov.: 31 AF XY: 0.326 AC XY: 24236 AN XY: 74244

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.295

Alfa AF: 0.228 Hom.: 6682

Bravo AF: 0.342

Asia WGS AF: 0.246 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6450023; hg19: chr5-68526063;