chr11-119422002-T-C

Position:

• chr11-119422002-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006288.5(THY1):​c.-24-1073A>G variant causes a intron 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_006288.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

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 -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
THY1	NM_006288.5	c.-24-1073A>G		intron_variant		ENST00000284240.10
USP2-AS1	NR_034160.1	n.305+26848T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THY1	ENST00000284240.10	c.-24-1073A>G		intron_variant		1	NM_006288.5	P1
USP2-AS1	ENST00000706409.1	n.252-47807T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.357

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

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.558

Gnomad4 ASJ AF: 0.604

Gnomad4 EAS AF: 0.863

Gnomad4 SAS AF: 0.779

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.584

Alfa AF: 0.594 Hom.: 25806

Bravo AF: 0.542

Asia WGS AF: 0.777 AC: 2697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.49

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: rs1001205; hg19: chr11-119292712;