rs140649985

Variant names:

• chr6-167373198-C-A
• rs140649985
• ENST00000397829.8:n.1120G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-167373198-C-A
• chr6-167373198-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000397829.8(TCP10L3):​n.1120G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 41)
• Consequence: TCP10L3 ENST00000397829.8 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913

Genes affected

TCP10L3 (HGNC:):

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

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.10169393).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCP10L3	NR_163193.1	n.1018G>T		non_coding_transcript_exon_variant	Exon 6 of 6
TCP10L3	NR_163194.1	n.1164G>T		non_coding_transcript_exon_variant	Exon 8 of 8
TCP10L3	NR_163195.1	n.1091G>T		non_coding_transcript_exon_variant	Exon 7 of 7
TCP10L3	NR_163196.1	n.803G>T		non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCP10L3	ENST00000397829.8	n.1120G>T		non_coding_transcript_exon_variant	Exon 8 of 8	1
TCP10L3	ENST00000514083.1	n.1614G>T		non_coding_transcript_exon_variant	Exon 2 of 2	1
TCP10L3	ENST00000463894.7	n.3399G>T		non_coding_transcript_exon_variant	Exon 6 of 6	2

Frequencies

GnomAD3 genomes Cov.: 41

GnomAD3 exomes AF: 0.00000403 AC: 1 AN: 247960 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 134532

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.000166

GnomAD4 exome Cov.: 88

GnomAD4 genome Cov.: 41

ExAC AF: 0.00000828 AC: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.31	T
BayesDel_noAF	Benign	-0.68
CADD	Benign	0.14
DANN	Uncertain	0.99
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.020	N
LIST_S2	Benign	0.38	T;T;T
M_CAP	Benign	0.0016	T
MetaRNN	Benign	0.10	T;T;T
MetaSVM	Benign	-1.0	T
PrimateAI	Benign	0.30	T
PROVEAN	Benign	0.35	N;.;.
REVEL	Benign	0.013
Sift	Pathogenic	0.0	D;.;.
Sift4G	Pathogenic	0.0	D;D;.
Vest4		0.072
MVP		0.088
MPC		0.80
ClinPred		0.31	T
GERP RS		-3.3
gMVP		0.024

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: rs140649985; hg19: chr6-167786686;