rs16827043

Variant names:

• chr1-146039555-C-T
• rs16827043
• unassigned_transcript_158:c.*82C>T

Variant summary

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

The ENST00000000000(TRK-CTT2-1):​c.*82C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.887 in 152,226 control chromosomes in the GnomAD database, including 60,037 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 0.89 (60037 hom., cov: 31)
• Consequence: TRK-CTT2-1 ENST00000000000 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.977
• Publications: 12 publications found

Genes affected

TRK-CTT2-1 (HGNC:34761):

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 (AMR) allele frequency at 95% confidence interval = 0.892 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: 0.887 AC: 134929 AN: 152108 Hom.: 59991 Cov.: 31

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.887 AC: 135028 AN: 152226 Hom.: 60037 Cov.: 31 AF XY: 0.887 AC XY: 66001 AN XY: 74422

African (AFR) AF: 0.880 AC: 36525 AN: 41516

American (AMR) AF: 0.904 AC: 13829 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2731 AN: 3472

East Asian (EAS) AF: 0.782 AC: 4047 AN: 5172

South Asian (SAS) AF: 0.870 AC: 4202 AN: 4828

European-Finnish (FIN) AF: 0.929 AC: 9855 AN: 10606

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.896 AC: 60967 AN: 68024

Other (OTH) AF: 0.875 AC: 1848 AN: 2112

Alfa AF: 0.887 Hom.: 164551

Bravo AF: 0.884

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	0.097
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs16827043; hg19: chr1-145395440;