ENST00000435042.1:n.94+995T>C

Variant names:

• chr5-132663184-A-G
• rs1295683
• ENST00000435042.1:n.94+995T>C

Variant summary

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

The ENST00000435042.1(TH2LCRR):​n.94+995T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.868 in 152,178 control chromosomes in the GnomAD database, including 57,608 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 0.87 (57608 hom., cov: 31)
• Consequence: TH2LCRR ENST00000435042.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.626
• Publications: 24 publications found

Genes affected

TH2LCRR (HGNC:40495): (T helper type 2 locus control region associated RNA)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435042.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TH2LCRR	ENST00000435042.1	TSL:5	n.94+995T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.868 AC: 132016 AN: 152060 Hom.: 57569 Cov.: 31

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.879

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.868 AC: 132107 AN: 152178 Hom.: 57608 Cov.: 31 AF XY: 0.860 AC XY: 63964 AN XY: 74390

African (AFR) AF: 0.898 AC: 37286 AN: 41518

American (AMR) AF: 0.790 AC: 12090 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3012 AN: 3472

East Asian (EAS) AF: 0.819 AC: 4226 AN: 5162

South Asian (SAS) AF: 0.864 AC: 4163 AN: 4816

European-Finnish (FIN) AF: 0.730 AC: 7730 AN: 10592

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.892 AC: 60644 AN: 68000

Other (OTH) AF: 0.878 AC: 1858 AN: 2116

Alfa AF: 0.875 Hom.: 11544

Bravo AF: 0.872

Asia WGS AF: 0.827 AC: 2879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.7
DANN	Benign	0.67
PhyloP100		0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1295683; hg19: chr5-131998876;