6-52192184-A-G

Position:

• chr6-52192184-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 0.612 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.735

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.763

Gnomad4 OTH AF: 0.642

Alfa AF: 0.675 Hom.: 4783

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1892280; hg19: chr6-52056982;