rs2345794

Variant names:

• chr6-167376565-C-G
• rs2345794
• ENST00000397829.8:n.725G>C

Your query was ambiguous. Multiple possible variants found:

• chr6-167376565-C-G
• chr6-167376565-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000397829.8(TCP10L3):​n.725G>C 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 4)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TCP10L3 ENST00000397829.8 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396

Genes affected

TCP10L3 (HGNC:):

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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.05909109).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCP10L3	NR_163193.1	n.623G>C		non_coding_transcript_exon_variant	Exon 3 of 6
TCP10L3	NR_163194.1	n.769G>C		non_coding_transcript_exon_variant	Exon 5 of 8
TCP10L3	NR_163195.1	n.696G>C		non_coding_transcript_exon_variant	Exon 4 of 7
TCP10L3	NR_163196.1	n.408G>C		non_coding_transcript_exon_variant	Exon 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCP10L3	ENST00000397829.8	n.725G>C		non_coding_transcript_exon_variant	Exon 5 of 8	1
TCP10L3	ENST00000460930.2	n.545G>C		non_coding_transcript_exon_variant	Exon 3 of 3	1
TCP10L3	ENST00000366827.6	n.769G>C		non_coding_transcript_exon_variant	Exon 5 of 9	5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 59388 Hom.: 0 Cov.: 4 FAILED QC

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 789066 Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0 AN XY: 391038

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 59388 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 28766

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.37	T
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.2
DANN	Benign	0.075
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.010	N
LIST_S2	Benign	0.52	.;T;T
M_CAP	Benign	0.0012	T
MetaRNN	Benign	0.059	T;T;T
MetaSVM	Benign	-1.0	T
PrimateAI	Benign	0.34	T
PROVEAN	Benign	0.24	N;N;.
REVEL	Benign	0.037
Sift	Benign	1.0	T;T;.
Sift4G	Benign	0.18	T;T;T
Polyphen		0.018	.;B;.
Vest4		0.11
MVP		0.014
MPC		2.2
ClinPred		0.035	T
GERP RS		-3.3
gMVP		0.050

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: rs2345794; hg19: chr6-167790053;