rs569189

Variant names:

• chr6-54442382-A-G
• rs569189

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.148 AC: 6133 AN: 41416

American (AMR) AF: 0.0534 AC: 816 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0542 AC: 188 AN: 3470

East Asian (EAS) AF: 0.101 AC: 522 AN: 5156

South Asian (SAS) AF: 0.0592 AC: 285 AN: 4816

European-Finnish (FIN) AF: 0.0440 AC: 467 AN: 10612

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0627 AC: 4260 AN: 67970

Other (OTH) AF: 0.0640 AC: 135 AN: 2110

Alfa AF: 0.0790 Hom.: 58

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
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs569189; hg19: chr6-54307180;