Genetic Variant THY1:c.*84C>G (chr11-119419324-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_006288.5(THY1):c.*84C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 1,223,372 control chromosomes in the GnomAD database, including 231,720 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 0.55 ( 24052 hom., cov: 31)

Exomes 𝑓: 0.62 ( 207668 hom. )

Consequence

THY1
NM_006288.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00700

Variant links:

Genes affected

THY1 (HGNC:11801): (Thy-1 cell surface antigen) This gene encodes a cell surface glycoprotein and member of the immunoglobulin superfamily of proteins. The encoded protein is involved in cell adhesion and cell communication in numerous cell types, but particularly in cells of the immune and nervous systems. The encoded protein is widely used as a marker for hematopoietic stem cells. This gene may function as a tumor suppressor in nasopharyngeal carcinoma. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]

THY1 links:

USP2-AS1 (HGNC:48673): (USP2 antisense RNA 1)

USP2-AS1 links:

THY1-AS1 (HGNC:54852): (THY1 antisense RNA 1)

THY1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=6.936216E-7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THY1	NM_006288.5 link	c.*84C>G		3_prime_UTR_variant	Exon 4 of 4	ENST00000284240.10	NP_006279.2	P04216B0YJA4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THY1	ENST00000284240 link	c.*84C>G		3_prime_UTR_variant	Exon 4 of 4	1	NM_006288.5	ENSP00000284240.6		P04216

Frequencies

GnomAD3 genomes

AF:

0.549

AC:

83307

AN:

151828

Hom.:

24048

Cov.:

show subpopulations

Gnomad AFR

AF:

0.375

Gnomad AMI

AF:

0.677

Gnomad AMR

AF:

0.557

Gnomad ASJ

AF:

0.605

Gnomad EAS

AF:

0.865

Gnomad SAS

AF:

0.780

Gnomad FIN

AF:

0.583

Gnomad MID

AF:

0.671

Gnomad NFE

AF:

0.600

Gnomad OTH

AF:

0.580

GnomAD3 exomes

AF:

0.632

AC:

104444

AN:

165350

Hom.:

33845

AF XY:

0.645

AC XY:

56849

AN XY:

88118

show subpopulations

Gnomad AFR exome

AF:

0.375

Gnomad AMR exome

AF:

0.598

Gnomad ASJ exome

AF:

0.600

Gnomad EAS exome

AF:

0.865

Gnomad SAS exome

AF:

0.776

Gnomad FIN exome

AF:

0.585

Gnomad NFE exome

AF:

0.600

Gnomad OTH exome

AF:

0.635

GnomAD4 exome

AF:

0.616

AC:

659797

AN:

1071426

Hom.:

207668

Cov.:

AF XY:

0.623

AC XY:

338805

AN XY:

543694

show subpopulations

Gnomad4 AFR exome

AF:

0.371

Gnomad4 AMR exome

AF:

0.598

Gnomad4 ASJ exome

AF:

0.601

Gnomad4 EAS exome

AF:

0.848

Gnomad4 SAS exome

AF:

0.778

Gnomad4 FIN exome

AF:

0.586

Gnomad4 NFE exome

AF:

0.601

Gnomad4 OTH exome

AF:

0.619

GnomAD4 genome

AF:

0.548

AC:

83335

AN:

151946

Hom.:

24052

Cov.:

AF XY:

0.556

AC XY:

41265

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.375

Gnomad4 AMR

AF:

0.556

Gnomad4 ASJ

AF:

0.605

Gnomad4 EAS

AF:

0.865

Gnomad4 SAS

AF:

0.780

Gnomad4 FIN

AF:

0.583

Gnomad4 NFE

AF:

0.600

Gnomad4 OTH

AF:

0.583

Alfa

AF:

0.523

Hom.:

2930

Bravo

AF:

0.539

TwinsUK

AF:

0.594

AC:

2201

ALSPAC

AF:

0.587

AC:

2263

ExAC

AF:

0.552

AC:

59478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.57

CADD

Benign

0.29

DANN

Benign

0.35

DEOGEN2

Benign

0.0071

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.067

LIST_S2

Benign

0.24

MetaRNN

Benign

6.9e-7

MetaSVM

Benign

-1.1

PROVEAN

Benign

0.31

REVEL

Benign

0.039

Sift

Pathogenic

0.0

ClinPred

0.013

GERP RS

2.0

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