6-167376672-C-T

Position:

• chr6-167376672-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NR_163196.1(TCP10L3):​n.301G>A 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 0.0018 (0 hom., cov: 9)
  • Exomes 𝑓: 0.0030 (2 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: -1.51

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP6: Variant 6-167376672-C-T is Benign according to our data. Variant chr6-167376672-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 769701.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.301G>A		non_coding_transcript_exon_variant	3/6
TCP10L3	NR_163193.1	n.516G>A		non_coding_transcript_exon_variant	3/6
TCP10L3	NR_163194.1	n.662G>A		non_coding_transcript_exon_variant	5/8
TCP10L3	NR_163195.1	n.589G>A		non_coding_transcript_exon_variant	4/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TCP10L3	ENST00000366827.6	n.662G>A		non_coding_transcript_exon_variant	5/9	5
TCP10L3	ENST00000675664.1	n.531G>A		non_coding_transcript_exon_variant	4/9

Frequencies

GnomAD3 genomes AF: 0.00 AC: 129 AN: 74168 Hom.: 0 Cov.: 9 FAILED QC

Gnomad AFR AF: 0.00102

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00911

Gnomad ASJ AF: 0.000582

Gnomad EAS AF: 0.00899

Gnomad SAS AF: 0.00428

Gnomad FIN AF: 0.000227

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000409

Gnomad OTH AF: 0.00746

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00299 AC: 2471 AN: 826396 Hom.: 2 Cov.: 12 AF XY: 0.00319 AC XY: 1330 AN XY: 416298

Gnomad4 AFR exome AF: 0.00192

Gnomad4 AMR exome AF: 0.0272

Gnomad4 ASJ exome AF: 0.000957

Gnomad4 EAS exome AF: 0.0197

Gnomad4 SAS exome AF: 0.00668

Gnomad4 FIN exome AF: 0.00166

Gnomad4 NFE exome AF: 0.00134

Gnomad4 OTH exome AF: 0.00313

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00177 AC: 131 AN: 74206 Hom.: 0 Cov.: 9 AF XY: 0.00188 AC XY: 65 AN XY: 34624

Gnomad4 AFR AF: 0.00107

Gnomad4 AMR AF: 0.00911

Gnomad4 ASJ AF: 0.000582

Gnomad4 EAS AF: 0.00901

Gnomad4 SAS AF: 0.00429

Gnomad4 FIN AF: 0.000227

Gnomad4 NFE AF: 0.000409

Gnomad4 OTH AF: 0.00849

Alfa AF: 0.00464 Hom.: 0

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

Labcorp Genetics (formerly Invitae), Labcorp

Mar 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.50

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.24		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.24		Position offset: 32

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

Publications

LitVar

Other links and lift over

dbSNP: rs200905775; hg19: chr6-167790160; COSMIC: COSV64751205; COSMIC: COSV64751205;