rs3138076

Variant names:

• chr5-140635028-T-C
• rs3138076
• XM_011537665.3:c.-129-6637T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-140635028-T-C
• chr5-140635028-T-G

Variant summary

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

The XM_011537665.3(TMCO6):​c.-129-6637T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 151,256 control chromosomes in the GnomAD database, including 4,240 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 0.23 (4240 hom., cov: 33)
• Consequence: TMCO6 XM_011537665.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.730
• Publications: 10 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35174 AN: 151134 Hom.: 4225 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.0547

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.163

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.233 AC: 35202 AN: 151256 Hom.: 4240 Cov.: 33 AF XY: 0.235 AC XY: 17364 AN XY: 73918

African (AFR) AF: 0.190 AC: 7803 AN: 41140

American (AMR) AF: 0.238 AC: 3625 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 727 AN: 3462

East Asian (EAS) AF: 0.298 AC: 1522 AN: 5100

South Asian (SAS) AF: 0.262 AC: 1249 AN: 4770

European-Finnish (FIN) AF: 0.309 AC: 3249 AN: 10516

Middle Eastern (MID) AF: 0.154 AC: 43 AN: 280

European-Non Finnish (NFE) AF: 0.243 AC: 16435 AN: 67772

Other (OTH) AF: 0.239 AC: 500 AN: 2096

Alfa AF: 0.234 Hom.: 503

Bravo AF: 0.223

Asia WGS AF: 0.319 AC: 1109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.46
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs3138076; hg19: chr5-140014613;