Variant rs3798324 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000397829.8(TCP10L3):n.1232T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0608 in 1,538,184 control chromosomes in the GnomAD database, including 20 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 0.055 ( 0 hom., cov: 41)

Exomes 𝑓: 0.061 ( 20 hom. )

Consequence

TCP10L3
ENST00000397829.8 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.208

Variant links:

Genes affected

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

TCP10L3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	Effect
TCP10L3	NR_163196.1 linkuse as main transcript	downstream_gene_variant
TCP10L3	NR_163193.1 linkuse as main transcript	downstream_gene_variant
TCP10L3	NR_163194.1 linkuse as main transcript	downstream_gene_variant
TCP10L3	NR_163195.1 linkuse as main transcript	downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TCP10L3	ENST00000366827.6 linkuse as main transcript	n.1001+1265T>A		intron_variant, non_coding_transcript_variant		5
TCP10L3	ENST00000675664.1 linkuse as main transcript	n.762+170T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0552

AC:

8345

AN:

151258

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0222

Gnomad AMI

AF:

0.0422

Gnomad AMR

AF:

0.0833

Gnomad ASJ

AF:

0.0838

Gnomad EAS

AF:

0.215

Gnomad SAS

AF:

0.104

Gnomad FIN

AF:

0.0550

Gnomad MID

AF:

0.0255

Gnomad NFE

AF:

0.0525

Gnomad OTH

AF:

0.0550

GnomAD4 exome

AF:

0.0614

AC:

85142

AN:

1386812

Hom.:

Cov.:

AF XY:

0.0623

AC XY:

42593

AN XY:

684150

show subpopulations

Gnomad4 AFR exome

AF:

0.0196

Gnomad4 AMR exome

AF:

0.106

Gnomad4 ASJ exome

AF:

0.0938

Gnomad4 EAS exome

AF:

0.195

Gnomad4 SAS exome

AF:

0.107

Gnomad4 FIN exome

AF:

0.0614

Gnomad4 NFE exome

AF:

0.0524

Gnomad4 OTH exome

AF:

0.0702

GnomAD4 genome

AF:

0.0552

AC:

8362

AN:

151372

Hom.:

Cov.:

AF XY:

0.0582

AC XY:

4304

AN XY:

73988

show subpopulations

Gnomad4 AFR

AF:

0.0224

Gnomad4 AMR

AF:

0.0837

Gnomad4 ASJ

AF:

0.0838

Gnomad4 EAS

AF:

0.216

Gnomad4 SAS

AF:

0.103

Gnomad4 FIN

AF:

0.0550

Gnomad4 NFE

AF:

0.0525

Gnomad4 OTH

AF:

0.0554

Alfa

AF:

0.0523

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

2.7

DANN

Benign

0.39

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over