rs2243204

chr5-132663802-C-T

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TH2LCRR	ENST00000435042.1	n.94+377G>A		intron_variant, non_coding_transcript_variant		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;