11-119419324-G-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• 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 -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.

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>G		3_prime_UTR	Exon 4 of 4	NP_006279.2
	THY1	NM_001311160.2		c.*84C>G		3_prime_UTR	Exon 4 of 4	NP_001298089.1	P04216
	THY1	NM_001311162.2		c.*84C>G		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>G		3_prime_UTR	Exon 4 of 4	ENSP00000284240.6	P04216
	THY1	ENST00000524970.5	TSL:4	c.481C>G	p.Pro161Ala	missense	Exon 4 of 4	ENSP00000432808.1	E9PNQ8
	THY1	ENST00000918469.1		c.*84C>G		3_prime_UTR	Exon 4 of 4	ENSP00000588528.1

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83307 AN: 151828 Hom.: 24048 Cov.: 31

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

GnomAD2 exomes AF: 0.632 AC: 104444 AN: 165350 AF XY: 0.645

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 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.: 14 AF XY: 0.623 AC XY: 338805 AN XY: 543694

African (AFR) AF: 0.371 AC: 9468 AN: 25526

American (AMR) AF: 0.598 AC: 21324 AN: 35686

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 13933 AN: 23178

East Asian (EAS) AF: 0.848 AC: 29530 AN: 34806

South Asian (SAS) AF: 0.778 AC: 56759 AN: 72930

European-Finnish (FIN) AF: 0.586 AC: 28807 AN: 49186

Middle Eastern (MID) AF: 0.659 AC: 3331 AN: 5054

European-Non Finnish (NFE) AF: 0.601 AC: 467316 AN: 777680

Other (OTH) AF: 0.619 AC: 29329 AN: 47380

GnomAD4 genome AF: 0.548 AC: 83335 AN: 151946 Hom.: 24052 Cov.: 31 AF XY: 0.556 AC XY: 41265 AN XY: 74270

African (AFR) AF: 0.375 AC: 15541 AN: 41436

American (AMR) AF: 0.556 AC: 8497 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2099 AN: 3472

East Asian (EAS) AF: 0.865 AC: 4452 AN: 5148

South Asian (SAS) AF: 0.780 AC: 3761 AN: 4824

European-Finnish (FIN) AF: 0.583 AC: 6155 AN: 10558

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.600 AC: 40785 AN: 67920

Other (OTH) AF: 0.583 AC: 1230 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.055
BayesDel_addAF	Benign	-0.66	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	0.29
DANN	Benign	0.35
DEOGEN2	Benign	0.0071	T
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.067	N
LIST_S2	Benign	0.24	T
MetaRNN	Benign	6.9e-7	T
MetaSVM	Benign	-1.1	T
PhyloP100		0.0070
PROVEAN	Benign	0.31	N
REVEL	Benign	0.039
Sift	Pathogenic	0.0	D
ClinPred		0.013	T
GERP RS		2.0
Mutation Taster		=100/0	polymorphism (auto)

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; COSMIC: COSV52454640; COSMIC: COSV52454640;