rs569189

chr6-54442382-A-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 0.0847 in 152,038 control chromosomes in the GnomAD database, including 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 0.085 (676 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.145 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: 0.0847 AC: 12869 AN: 151920 Hom.: 678 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0536

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0595

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0627

Gnomad OTH AF: 0.0632

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

GnomAD4 genome AF: 0.0847 AC: 12873 AN: 152038 Hom.: 676 Cov.: 32 AF XY: 0.0822 AC XY: 6113 AN XY: 74356

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.0534

Gnomad4 ASJ AF: 0.0542

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.0592

Gnomad4 FIN AF: 0.0440

Gnomad4 NFE AF: 0.0627

Gnomad4 OTH AF: 0.0640

Alfa AF: 0.0760 Hom.: 51

Bravo AF: 0.0871

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	11
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs569189; hg19: chr6-54307180;