6-27592808-A-G

Position:

• chr6-27592808-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.536 in 151,936 control chromosomes in the GnomAD database, including 23,321 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 (23321 hom., cov: 31)
• Consequence: TRX-CAT1-6 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.811

Genes affected

TRX-CAT1-6 (HGNC:34863):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRX-CAT1-6	unassigned_transcript_1029	c.*13T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81460 AN: 151818 Hom.: 23319 Cov.: 31

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.536 AC: 81494 AN: 151936 Hom.: 23321 Cov.: 31 AF XY: 0.536 AC XY: 39819 AN XY: 74250

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.739

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.563

Alfa AF: 0.616 Hom.: 37138

Bravo AF: 0.523

Asia WGS AF: 0.516 AC: 1795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	2.1
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10946940; hg19: chr6-27560587;