rs1054735

Variant names:

• chr11-119419324-G-A
• rs1054735
• NM_006288.5:c.*84C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-119419324-G-A
• chr11-119419324-G-C
• chr11-119419324-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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)

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

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0036794245).
• BS2: High Homozygotes in GnomAd4 at 3 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006288.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THY1	NM_006288.5	MANE Select	c.*84C>T		3_prime_UTR	Exon 4 of 4	NP_006279.2
	THY1	NM_001311160.2		c.*84C>T		3_prime_UTR	Exon 4 of 4	NP_001298089.1	P04216
	THY1	NM_001311162.2		c.*84C>T		3_prime_UTR	Exon 4 of 4	NP_001298091.1	P04216

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THY1	ENST00000284240.10	TSL:1 MANE Select	c.*84C>T		3_prime_UTR	Exon 4 of 4	ENSP00000284240.6	P04216
	THY1	ENST00000524970.5	TSL:4	c.481C>T	p.Pro161Ser	missense	Exon 4 of 4	ENSP00000432808.1	E9PNQ8
	THY1	ENST00000918469.1		c.*84C>T		3_prime_UTR	Exon 4 of 4	ENSP00000588528.1

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

GnomAD2 exomes AF: 0.000575 AC: 95 AN: 165350 AF XY: 0.000465

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 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

African (AFR) AF: 0.0111 AC: 283 AN: 25568

American (AMR) AF: 0.000364 AC: 13 AN: 35694

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23194

East Asian (EAS) AF: 0.00 AC: 0 AN: 34810

South Asian (SAS) AF: 0.0000137 AC: 1 AN: 72944

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 49218

Middle Eastern (MID) AF: 0.000989 AC: 5 AN: 5054

European-Non Finnish (NFE) AF: 0.00000898 AC: 7 AN: 779164

Other (OTH) AF: 0.000590 AC: 28 AN: 47438

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

African (AFR) AF: 0.0109 AC: 450 AN: 41456

American (AMR) AF: 0.000655 AC: 10 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5148

South Asian (SAS) AF: 0.00 AC: 0 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10570

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000147 AC: 1 AN: 67942

Other (OTH) AF: 0.00142 AC: 3 AN: 2112

Alfa AF: 0.000216 Hom.: 2930

ExAC AF: 0.000789 AC: 85

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.069
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
PhyloP100		0.0070
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
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs1054735; hg19: chr11-119290034;