XM_011537665.3:c.-129-6873C>T

Variant names:

• chr5-140634792-C-T
• rs2915863
• XM_011537665.3:c.-129-6873C>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.-129-6873C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 150,346 control chromosomes in the GnomAD database, including 31,665 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 0.64 (31665 hom., cov: 29)
• Consequence: TMCO6 XM_011537665.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34
• Publications: 26 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 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: 0.644 AC: 96796 AN: 150224 Hom.: 31602 Cov.: 29

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.645 AC: 96919 AN: 150346 Hom.: 31665 Cov.: 29 AF XY: 0.644 AC XY: 47330 AN XY: 73452

African (AFR) AF: 0.773 AC: 31799 AN: 41160

American (AMR) AF: 0.606 AC: 9148 AN: 15088

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2032 AN: 3444

East Asian (EAS) AF: 0.492 AC: 2444 AN: 4970

South Asian (SAS) AF: 0.524 AC: 2471 AN: 4718

European-Finnish (FIN) AF: 0.686 AC: 7121 AN: 10388

Middle Eastern (MID) AF: 0.616 AC: 165 AN: 268

European-Non Finnish (NFE) AF: 0.597 AC: 40212 AN: 67360

Other (OTH) AF: 0.629 AC: 1310 AN: 2082

Alfa AF: 0.613 Hom.: 3417

Bravo AF: 0.636

Asia WGS AF: 0.585 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.72
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs2915863; hg19: chr5-140014377; COSMIC: COSV52800011;