rs7721577

Variant names:

• chr5-140626201-T-C
• rs7721577
• XM_011537665.3:c.-129-15464T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-140626201-T-C
• chr5-140626201-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.-129-15464T>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
• Publications: 19 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 = 0.285 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.0854 AC: 3516 AN: 41160

American (AMR) AF: 0.219 AC: 3328 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 708 AN: 3472

East Asian (EAS) AF: 0.298 AC: 1537 AN: 5164

South Asian (SAS) AF: 0.256 AC: 1234 AN: 4812

European-Finnish (FIN) AF: 0.285 AC: 2962 AN: 10404

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15777 AN: 67898

Other (OTH) AF: 0.202 AC: 426 AN: 2108

Alfa AF: 0.217 Hom.: 6230

Bravo AF: 0.183

Asia WGS AF: 0.318 AC: 1105 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	0.98
DANN	Benign	0.35
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs7721577; hg19: chr5-140005786;