rs9257445

Variant names:

• chr6-28981429-G-C
• rs9257445
• unassigned_transcript_1089:c.*243C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000000000(TRF-GAA1-2):​c.*243C>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,930 control chromosomes in the GnomAD database, including 10,197 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 0.34 (10197 hom., cov: 32)
• Consequence: TRF-GAA1-2 ENST00000000000 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 8 publications found

Genes affected

TRF-GAA1-2 (HGNC:34817):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51696 AN: 151812 Hom.: 10176 Cov.: 32

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.341 AC: 51754 AN: 151930 Hom.: 10197 Cov.: 32 AF XY: 0.343 AC XY: 25493 AN XY: 74264

African (AFR) AF: 0.541 AC: 22369 AN: 41384

American (AMR) AF: 0.290 AC: 4434 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1323 AN: 3468

East Asian (EAS) AF: 0.224 AC: 1161 AN: 5174

South Asian (SAS) AF: 0.362 AC: 1743 AN: 4816

European-Finnish (FIN) AF: 0.292 AC: 3078 AN: 10550

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16676 AN: 67958

Other (OTH) AF: 0.335 AC: 707 AN: 2108

Alfa AF: 0.295 Hom.: 1027

Bravo AF: 0.350

Asia WGS AF: 0.282 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	0.50
DANN	Benign	0.50
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9257445; hg19: chr6-28949206;