5-140606905-C-T

Variant names:

• chr5-140606905-C-T
• rs2163786
• XM_011537665.3:c.-130+10014C>T

Variant summary

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

The XM_011537665.3(TMCO6):​c.-130+10014C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,414 control chromosomes in the GnomAD database, including 18,801 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 0.49 (18801 hom., cov: 29)
• Consequence: TMCO6 XM_011537665.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960
• Publications: 18 publications found

Genes affected

TMCO6 (HGNC:28814): (transmembrane and coiled-coil domains 6) Predicted to enable nuclear import signal receptor activity. Predicted to be involved in protein import into nucleus. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.512 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: 0.493 AC: 74579 AN: 151294 Hom.: 18776 Cov.: 29

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.493 AC: 74660 AN: 151414 Hom.: 18801 Cov.: 29 AF XY: 0.498 AC XY: 36786 AN XY: 73936

African (AFR) AF: 0.432 AC: 17799 AN: 41194

American (AMR) AF: 0.495 AC: 7531 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1807 AN: 3468

East Asian (EAS) AF: 0.430 AC: 2212 AN: 5142

South Asian (SAS) AF: 0.461 AC: 2219 AN: 4810

European-Finnish (FIN) AF: 0.644 AC: 6724 AN: 10438

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35037 AN: 67854

Other (OTH) AF: 0.494 AC: 1036 AN: 2096

Alfa AF: 0.431 Hom.: 1959

Bravo AF: 0.475

Asia WGS AF: 0.495 AC: 1720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.66
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs2163786; hg19: chr5-139986490;