1-204506706-G-T

Variant names:

• chr1-204506706-G-T
• rs4951389
• unassigned_transcript_271:c.*107G>T

Variant summary

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

The ENST00000000000(TRK-TTT3-1):​c.*107G>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 151,986 control chromosomes in the GnomAD database, including 27,185 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 0.57 (27185 hom., cov: 32)
• Consequence: TRK-TTT3-1 ENST00000000000 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 13 publications found

Genes affected

TRK-TTT3-1 (HGNC:34684):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86590 AN: 151866 Hom.: 27181 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.570 AC: 86610 AN: 151986 Hom.: 27185 Cov.: 32 AF XY: 0.576 AC XY: 42795 AN XY: 74270

African (AFR) AF: 0.284 AC: 11781 AN: 41432

American (AMR) AF: 0.597 AC: 9111 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2130 AN: 3472

East Asian (EAS) AF: 0.681 AC: 3517 AN: 5168

South Asian (SAS) AF: 0.607 AC: 2930 AN: 4824

European-Finnish (FIN) AF: 0.794 AC: 8384 AN: 10558

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.687 AC: 46698 AN: 67960

Other (OTH) AF: 0.572 AC: 1206 AN: 2108

Alfa AF: 0.649 Hom.: 13175

Bravo AF: 0.543

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	1.9
DANN	Benign	0.35
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs4951389; hg19: chr1-204475834;