1-146039391-A-G

Variant names:

• chr1-146039391-A-G
• rs12091564
• unassigned_transcript_158:c.-10A>G

Variant summary

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

The ENST00000000000(TRK-CTT2-1):​c.-10A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,252 control chromosomes in the GnomAD database, including 2,964 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 0.15 (2964 hom., cov: 32)
• Consequence: TRK-CTT2-1 ENST00000000000 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -7.54
• Publications: 19 publications found

Genes affected

TRK-CTT2-1 (HGNC:34761):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22114 AN: 152134 Hom.: 2955 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0418

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0546

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0405

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.146 AC: 22162 AN: 152252 Hom.: 2964 Cov.: 32 AF XY: 0.146 AC XY: 10890 AN XY: 74440

African (AFR) AF: 0.342 AC: 14206 AN: 41500

American (AMR) AF: 0.169 AC: 2589 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0418 AC: 145 AN: 3472

East Asian (EAS) AF: 0.176 AC: 913 AN: 5188

South Asian (SAS) AF: 0.129 AC: 624 AN: 4828

European-Finnish (FIN) AF: 0.0546 AC: 580 AN: 10622

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0405 AC: 2758 AN: 68032

Other (OTH) AF: 0.128 AC: 269 AN: 2108

Alfa AF: 0.0761 Hom.: 3204

Bravo AF: 0.163

Asia WGS AF: 0.207 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	0.0010
DANN	Benign	0.19
PhyloP100		-7.5

Splicing

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

Other links and lift over

dbSNP: rs12091564; hg19: chr1-145395604;