6-167376666-T-C

Position:

• chr6-167376666-T-C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NR_163196.1(TCP10L3):​n.307A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00033 (3 hom., cov: 9)
  • Exomes 𝑓: 0.00034 (41 hom.)
  • Failed GnomAD Quality Control
• Consequence: TCP10L3 NR_163196.1 non_coding_transcript_exon
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.389

Genes affected

TCP10L3 (HGNC:11656): (t-complex 10 like 3 (pseudogene))

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BP6: Variant 6-167376666-T-C is Benign according to our data. Variant chr6-167376666-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2657131.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TCP10L3	NR_163196.1	n.307A>G		non_coding_transcript_exon_variant	3/6
TCP10L3	NR_163193.1	n.522A>G		non_coding_transcript_exon_variant	3/6
TCP10L3	NR_163194.1	n.668A>G		non_coding_transcript_exon_variant	5/8
TCP10L3	NR_163195.1	n.595A>G		non_coding_transcript_exon_variant	4/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TCP10L3	ENST00000366827.6	n.668A>G		non_coding_transcript_exon_variant	5/9	5
TCP10L3	ENST00000675664.1	n.537A>G		non_coding_transcript_exon_variant	4/9

Frequencies

GnomAD3 genomes AF: 0.00 AC: 26 AN: 75772 Hom.: 3 Cov.: 9 FAILED QC

Gnomad AFR AF: 0.0000500

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00205

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00119

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00510

Gnomad NFE AF: 0.000189

Gnomad OTH AF: 0.00208

GnomAD3 exomes AF: 0.000629 AC: 62 AN: 98518 Hom.: 16 AF XY: 0.000724 AC XY: 38 AN XY: 52496

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00122

Gnomad ASJ exome AF: 0.00496

Gnomad EAS exome AF: 0.000111

Gnomad SAS exome AF: 0.000856

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000393

Gnomad OTH exome AF: 0.00145

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000342 AC: 289 AN: 846158 Hom.: 41 Cov.: 13 AF XY: 0.000350 AC XY: 149 AN XY: 426288

Gnomad4 AFR exome AF: 0.000328

Gnomad4 AMR exome AF: 0.000943

Gnomad4 ASJ exome AF: 0.00195

Gnomad4 EAS exome AF: 0.0000359

Gnomad4 SAS exome AF: 0.000347

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000257

Gnomad4 OTH exome AF: 0.000589

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000330 AC: 25 AN: 75818 Hom.: 3 Cov.: 9 AF XY: 0.000309 AC XY: 11 AN XY: 35556

Gnomad4 AFR AF: 0.0000498

Gnomad4 AMR AF: 0.00205

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000595

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000189

Gnomad4 OTH AF: 0.00207

Alfa AF: 0.000595 Hom.: 2

Bravo AF: 0.000230

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2023

TCP10L3: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.5
DANN	Benign	0.52

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs769668829; hg19: chr6-167790154;