5-140634792-C-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMCO6	XM_011537665.3	c.-129-6873C>T		intron_variant	Intron 1 of 10		XP_011535967.1
TMCO6	XM_047417355.1	c.-242-4947C>T		intron_variant	Intron 1 of 11		XP_047273311.1
TMCO6	XM_047417356.1	c.-255-4947C>T		intron_variant	Intron 1 of 11		XP_047273312.1

Ensembl

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

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 v4.3

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;