rs5744441

chr5-140637262-G-Achr5-140637262-G-C

Variant summary

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

The XM_011537665.3(TMCO6):c.-129-4403G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,106 control chromosomes in the GnomAD database, including 3,471 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 0.20 (3471 hom., cov: 32)
• Consequence: TMCO6 XM_011537665.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.812

Genes affected

TMCO6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMCO6	XM_011537665.3	c.-129-4403G>A		intron_variant
TMCO6	XM_024446125.2	c.-472-2477G>A		intron_variant
TMCO6	XM_047417355.1	c.-242-2477G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29821 AN: 151988 Hom.: 3458 Cov.: 32

Gnomad AFR AF: 0.0829

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.196 AC: 29844 AN: 152106 Hom.: 3471 Cov.: 32 AF XY: 0.199 AC XY: 14828 AN XY: 74328

Gnomad4 AFR AF: 0.0827

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.199

Alfa AF: 0.153 Hom.: 409

Bravo AF: 0.182

Asia WGS AF: 0.308 AC: 1072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.56
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5744441; hg19: chr5-140016847;