chr11-119419659-C-T

Position:

• chr11-119419659-C-T

Variant summary

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

The NM_006288.5(THY1):​c.374-139G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 665,294 control chromosomes in the GnomAD database, including 22,993 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 0.24 (4874 hom., cov: 33)
  • Exomes 𝑓: 0.26 (18119 hom.)
• Consequence: THY1 NM_006288.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352

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]

THY1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
THY1	NM_006288.5	c.374-139G>A		intron_variant		ENST00000284240.10	NP_006279.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
THY1	ENST00000284240.10	c.374-139G>A		intron_variant		1	NM_006288.5	ENSP00000284240.6

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36482 AN: 152066 Hom.: 4874 Cov.: 33

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.0865

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.257

GnomAD4 exome AF: 0.256 AC: 131456 AN: 513110 Hom.: 18119 Cov.: 6 AF XY: 0.249 AC XY: 67337 AN XY: 270000

Gnomad4 AFR exome AF: 0.135

Gnomad4 AMR exome AF: 0.308

Gnomad4 ASJ exome AF: 0.279

Gnomad4 EAS exome AF: 0.113

Gnomad4 SAS exome AF: 0.115

Gnomad4 FIN exome AF: 0.286

Gnomad4 NFE exome AF: 0.291

Gnomad4 OTH exome AF: 0.255

GnomAD4 genome AF: 0.240 AC: 36490 AN: 152184 Hom.: 4874 Cov.: 33 AF XY: 0.235 AC XY: 17512 AN XY: 74388

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.0867

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.255

Alfa AF: 0.276 Hom.: 1240

Bravo AF: 0.239

Asia WGS AF: 0.114 AC: 399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.38

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: rs1894006; hg19: chr11-119290369;