rs7721577

chr5-140626201-T-Cchr5-140626201-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.-129-15464T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 151,402 control chromosomes in the GnomAD database, including 3,425 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 (3425 hom., cov: 31)
• Consequence: TMCO6 XM_011537665.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40

Genes affected

TMCO6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMCO6	XM_011537665.3	c.-129-15464T>C		intron_variant
TMCO6	XM_024446125.2	c.-472-13538T>C		intron_variant
TMCO6	XM_047417355.1	c.-242-13538T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29552 AN: 151288 Hom.: 3413 Cov.: 31

Gnomad AFR AF: 0.0856

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.195 AC: 29575 AN: 151402 Hom.: 3425 Cov.: 31 AF XY: 0.197 AC XY: 14593 AN XY: 73926

Gnomad4 AFR AF: 0.0854

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.202

Alfa AF: 0.221 Hom.: 5072

Bravo AF: 0.183

Asia WGS AF: 0.318 AC: 1105 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	0.98
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7721577; hg19: chr5-140005786;