Variant rs1893261 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000529187.1(TLCD5):c.9G>A(p.Gln3=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 1,612,038 control chromosomes in the GnomAD database, including 120,016 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 0.40 ( 12265 hom., cov: 33)

Exomes 𝑓: 0.38 ( 107751 hom. )

Consequence

TLCD5
ENST00000529187.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.701

Variant links:

Genes affected

TLCD5 (HGNC:28280): (TLC domain containing 5) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TLCD5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP7

Synonymous conserved (PhyloP=-0.701 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TLCD5	NM_001198671.2 linkuse as main transcript	c.-1-57G>A		intron_variant		ENST00000375095.3	NP_001185600.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TLCD5	ENST00000375095.3 linkuse as main transcript	c.-1-57G>A		intron_variant		2	NM_001198671.2	ENSP00000364236	P1	Q6ZRR5-1

Frequencies

GnomAD3 genomes

AF:

0.398

AC:

60498

AN:

152000

Hom.:

12249

Cov.:

show subpopulations

Gnomad AFR

AF:

0.438

Gnomad AMI

AF:

0.321

Gnomad AMR

AF:

0.354

Gnomad ASJ

AF:

0.395

Gnomad EAS

AF:

0.281

Gnomad SAS

AF:

0.469

Gnomad FIN

AF:

0.472

Gnomad MID

AF:

0.361

Gnomad NFE

AF:

0.377

Gnomad OTH

AF:

0.379

GnomAD3 exomes

AF:

0.389

AC:

97580

AN:

251076

Hom.:

19278

AF XY:

0.392

AC XY:

53148

AN XY:

135692

show subpopulations

Gnomad AFR exome

AF:

0.437

Gnomad AMR exome

AF:

0.347

Gnomad ASJ exome

AF:

0.407

Gnomad EAS exome

AF:

0.282

Gnomad SAS exome

AF:

0.454

Gnomad FIN exome

AF:

0.467

Gnomad NFE exome

AF:

0.377

Gnomad OTH exome

AF:

0.399

GnomAD4 exome

AF:

0.382

AC:

557611

AN:

1459920

Hom.:

107751

Cov.:

AF XY:

0.384

AC XY:

278912

AN XY:

726358

show subpopulations

Gnomad4 AFR exome

AF:

0.436

Gnomad4 AMR exome

AF:

0.352

Gnomad4 ASJ exome

AF:

0.402

Gnomad4 EAS exome

AF:

0.268

Gnomad4 SAS exome

AF:

0.450

Gnomad4 FIN exome

AF:

0.471

Gnomad4 NFE exome

AF:

0.375

Gnomad4 OTH exome

AF:

0.390

GnomAD4 genome

AF:

0.398

AC:

60549

AN:

152118

Hom.:

12265

Cov.:

AF XY:

0.401

AC XY:

29782

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.439

Gnomad4 AMR

AF:

0.354

Gnomad4 ASJ

AF:

0.395

Gnomad4 EAS

AF:

0.281

Gnomad4 SAS

AF:

0.471

Gnomad4 FIN

AF:

0.472

Gnomad4 NFE

AF:

0.377

Gnomad4 OTH

AF:

0.374

Alfa

AF:

0.379

Hom.:

15096

Bravo

AF:

0.386

Asia WGS

AF:

0.428

AC:

1488

AN:

3478

EpiCase

AF:

0.367

EpiControl

AF:

0.371

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.3

DANN

Benign

0.28

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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