11-119422002-T-C

Variant names:

• chr11-119422002-T-C
• rs1001205
• NM_006288.5:c.-24-1073A>G

Variant summary

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

The NM_001311160.2(THY1):​c.-416A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 152,184 control chromosomes in the GnomAD database, including 24,326 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 (24325 hom., cov: 34)
  • Exomes 𝑓: 0.41 (1 hom.)
• Consequence: THY1 NM_001311160.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 6 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)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001311160.2. 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.-24-1073A>G		intron	N/A	NP_006279.2
	THY1	NM_001311160.2		c.-416A>G		5_prime_UTR	Exon 1 of 4	NP_001298089.1	P04216
	THY1	NM_001311162.2		c.-24-1073A>G		intron	N/A	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.-24-1073A>G		intron	N/A	ENSP00000284240.6	P04216
	THY1	ENST00000528522.5	TSL:2	c.-416A>G		5_prime_UTR	Exon 1 of 4	ENSP00000431301.1	P04216
	THY1	ENST00000900762.1		c.-1097A>G		5_prime_UTR	Exon 1 of 3	ENSP00000570821.1

Frequencies

GnomAD3 genomes AF: 0.553 AC: 84050 AN: 152044 Hom.: 24321 Cov.: 34

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.581

GnomAD4 exome AF: 0.409 AC: 9 AN: 22 Hom.: 1 Cov.: 0 AF XY: 0.389 AC XY: 7 AN XY: 18

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.357 AC: 5 AN: 14

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.553 AC: 84085 AN: 152162 Hom.: 24325 Cov.: 34 AF XY: 0.560 AC XY: 41639 AN XY: 74390

African (AFR) AF: 0.390 AC: 16183 AN: 41508

American (AMR) AF: 0.558 AC: 8534 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2097 AN: 3470

East Asian (EAS) AF: 0.863 AC: 4454 AN: 5162

South Asian (SAS) AF: 0.779 AC: 3768 AN: 4834

European-Finnish (FIN) AF: 0.582 AC: 6170 AN: 10596

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.601 AC: 40834 AN: 67982

Other (OTH) AF: 0.584 AC: 1234 AN: 2112

Alfa AF: 0.586 Hom.: 32406

Bravo AF: 0.542

Asia WGS AF: 0.777 AC: 2697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.49
PhyloP100		-1.5
Mutation Taster		=299/1	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: rs1001205; hg19: chr11-119292712;