chr5-140633982-T-G

Position:

• chr5-140633982-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_011537665.3(TMCO6):​c.-129-7683T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 151,624 control chromosomes in the GnomAD database, including 4,212 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 (4212 hom., cov: 30)
• Consequence: TMCO6 XM_011537665.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189

Genes affected

TMCO6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMCO6	XM_011537665.3	c.-129-7683T>G		intron_variant
TMCO6	XM_024446125.2	c.-472-5757T>G		intron_variant
TMCO6	XM_047417355.1	c.-242-5757T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35055 AN: 151506 Hom.: 4197 Cov.: 30

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.231 AC: 35083 AN: 151624 Hom.: 4212 Cov.: 30 AF XY: 0.233 AC XY: 17280 AN XY: 74064

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.236

Alfa AF: 0.128 Hom.: 227

Bravo AF: 0.222

Asia WGS AF: 0.320 AC: 1112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5744454; hg19: chr5-140013567;