rs1054735

chr11-119419324-G-Achr11-119419324-G-Cchr11-119419324-G-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_006288.5(THY1):c.*84C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000654 in 1,225,090 control chromosomes in the GnomAD database, including 5 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 0.0031 (3 hom., cov: 31)
  • Exomes 𝑓: 0.00031 (2 hom.)
• Consequence: THY1 NM_006288.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

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]

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

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0036794245).
• BS2: High Homozygotes in GnomAd at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
THY1	NM_006288.5	c.*84C>T		3_prime_UTR_variant	4/4	ENST00000284240.10
USP2-AS1	NR_034160.1	n.305+24170G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THY1	ENST00000284240.10	c.*84C>T		3_prime_UTR_variant	4/4	1	NM_006288.5	P1
USP2-AS1	ENST00000706409.1	n.252-50485G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00305 AC: 464 AN: 151888 Hom.: 3 Cov.: 31

Gnomad AFR AF: 0.0109

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000655

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: 0.0000147

Gnomad OTH AF: 0.00144

GnomAD3 exomes AF: 0.000575 AC: 95 AN: 165350 Hom.: 0 AF XY: 0.000465 AC XY: 41 AN XY: 88118

Gnomad AFR exome AF: 0.00923

Gnomad AMR exome AF: 0.000395

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: 0.0000151

Gnomad OTH exome AF: 0.000437

GnomAD4 exome AF: 0.000314 AC: 337 AN: 1073084 Hom.: 2 Cov.: 14 AF XY: 0.000252 AC XY: 137 AN XY: 544438

Gnomad4 AFR exome AF: 0.0111

Gnomad4 AMR exome AF: 0.000364

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000137

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000898

Gnomad4 OTH exome AF: 0.000590

GnomAD4 genome AF: 0.00305 AC: 464 AN: 152006 Hom.: 3 Cov.: 31 AF XY: 0.00292 AC XY: 217 AN XY: 74306

Gnomad4 AFR AF: 0.0109

Gnomad4 AMR AF: 0.000655

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00142

Alfa AF: 0.000216 Hom.: 2930

ExAC AF: 0.000789 AC: 85

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.56	T
BayesDel_noAF	Benign	-0.57
Cadd	Benign	1.0
Dann	Benign	0.45
DEOGEN2	Benign	0.0070	T
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.14	N
LIST_S2	Benign	0.26	T
MetaRNN	Benign	0.0037	T
MetaSVM	Benign	-0.58	T
MutationTaster	Benign	1.0	P;P
PROVEAN	Benign	0.16	N
REVEL	Benign	0.044
Sift	Pathogenic	0.0	D
MVP		0.28
ClinPred		0.023	T
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

Other links and lift over

dbSNP: rs1054735; hg19: chr11-119290034;