rs1894006

Variant names:

• chr11-119419659-C-A
• rs1894006
• NM_006288.5:c.374-139G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-119419659-C-A
• chr11-119419659-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_006288.5(THY1):​c.374-139G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000195 in 513,582 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0000019 (0 hom.)
• Consequence: THY1 NM_006288.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

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.374-139G>T		intron	N/A	NP_006279.2
	THY1	NM_001311160.2		c.374-139G>T		intron	N/A	NP_001298089.1	P04216
	THY1	NM_001311162.2		c.374-139G>T		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.374-139G>T		intron	N/A	ENSP00000284240.6	P04216
	THY1	ENST00000918469.1		c.530-139G>T		intron	N/A	ENSP00000588528.1
	THY1	ENST00000900759.1		c.410-139G>T		intron	N/A	ENSP00000570818.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000195 AC: 1 AN: 513582 Hom.: 0 Cov.: 6 AF XY: 0.00000370 AC XY: 1 AN XY: 270242

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 14004

American (AMR) AF: 0.00 AC: 0 AN: 22218

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14446

East Asian (EAS) AF: 0.00 AC: 0 AN: 32474

South Asian (SAS) AF: 0.00 AC: 0 AN: 49390

European-Finnish (FIN) AF: 0.0000220 AC: 1 AN: 45456

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2084

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 305432

Other (OTH) AF: 0.00 AC: 0 AN: 28078

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.46
DANN	Benign	0.48
PhyloP100		-0.35

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: rs1894006; hg19: chr11-119290369;