rs573301

chr6-23922478-C-G

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 0.54 in 151,978 control chromosomes in the GnomAD database, including 23,064 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 0.54 (23064 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.642 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: 0.540 AC: 81988 AN: 151860 Hom.: 23043 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.540 AC: 82050 AN: 151978 Hom.: 23064 Cov.: 32 AF XY: 0.526 AC XY: 39099 AN XY: 74288

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.500

Alfa AF: 0.554 Hom.: 2939

Bravo AF: 0.537

Asia WGS AF: 0.288 AC: 1005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.85
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs573301; hg19: chr6-23922706;