6-27592808-A-G

Variant names:

• chr6-27592808-A-G
• rs10946940
• unassigned_transcript_1029:c.*13T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000000000(TRX-CAT1-6):​c.*13T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. 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 ENST00000000000 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.811
• Publications: 27 publications found

Genes affected

TRX-CAT1-6 (HGNC:34863):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TRX-CAT1-6	unassigned_transcript_1029	c.*13T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.326 AC: 13513 AN: 41400

American (AMR) AF: 0.589 AC: 8992 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2565 AN: 3470

East Asian (EAS) AF: 0.511 AC: 2627 AN: 5142

South Asian (SAS) AF: 0.535 AC: 2580 AN: 4818

European-Finnish (FIN) AF: 0.612 AC: 6469 AN: 10566

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42867 AN: 67954

Other (OTH) AF: 0.563 AC: 1191 AN: 2114

Alfa AF: 0.605 Hom.: 86179

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
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs10946940; hg19: chr6-27560587;