ENST00000435042.1:n.94+377G>A

Variant names:

• chr5-132663802-C-T
• rs2243204
• ENST00000435042.1:n.94+377G>A

Variant summary

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

The ENST00000435042.1(TH2LCRR):​n.94+377G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,128 control chromosomes in the GnomAD database, including 7,461 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 0.23 (7461 hom., cov: 32)
• Consequence: TH2LCRR ENST00000435042.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.794

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TH2LCRR	ENST00000435042.1	n.94+377G>A		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.230 AC: 35032 AN: 152010 Hom.: 7428 Cov.: 32

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0712

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0848

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.231 AC: 35113 AN: 152128 Hom.: 7461 Cov.: 32 AF XY: 0.227 AC XY: 16878 AN XY: 74394

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0712

Gnomad4 NFE AF: 0.0849

Gnomad4 OTH AF: 0.193

Alfa AF: 0.115 Hom.: 2405

Bravo AF: 0.256

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.40
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243204; hg19: chr5-131999494;