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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRK-CTT2-1	unassigned_transcript_158	c.*82C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;