chr6-52192184-A-G

Variant names:

• chr6-52192184-A-G
• rs1892280

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 0.612 in 151,920 control chromosomes in the GnomAD database, including 32,250 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 0.61 (32250 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.758 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: 0.612 AC: 92917 AN: 151802 Hom.: 32242 Cov.: 31

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.612 AC: 92938 AN: 151920 Hom.: 32250 Cov.: 31 AF XY: 0.615 AC XY: 45648 AN XY: 74260

African (AFR) AF: 0.255 AC: 10578 AN: 41416

American (AMR) AF: 0.735 AC: 11230 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2162 AN: 3468

East Asian (EAS) AF: 0.691 AC: 3561 AN: 5156

South Asian (SAS) AF: 0.651 AC: 3116 AN: 4790

European-Finnish (FIN) AF: 0.772 AC: 8157 AN: 10560

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.763 AC: 51872 AN: 67948

Other (OTH) AF: 0.642 AC: 1354 AN: 2108

Alfa AF: 0.659 Hom.: 4806

Bravo AF: 0.594

Asia WGS AF: 0.652 AC: 2269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.9
DANN	Benign	0.79
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs1892280; hg19: chr6-52056982;