rs2243297

chr5-132663479-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000435042.1(TH2LCRR):n.94+700A>T 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 0.0273 in 152,262 control chromosomes in the GnomAD database, including 91 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 0.027 (91 hom., cov: 33)
• Consequence: TH2LCRR ENST00000435042.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

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=-0.65).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0273 (4150/152262) while in subpopulation NFE AF= 0.0406 (2761/67996). AF 95% confidence interval is 0.0393. There are 91 homozygotes in gnomad4. There are 2058 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 91 gene

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+700A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0273 AC: 4151 AN: 152144 Hom.: 91 Cov.: 33

Gnomad AFR AF: 0.00618

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.0252

Gnomad ASJ AF: 0.0518

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.0381

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0406

Gnomad OTH AF: 0.0325

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

GnomAD4 genome AF: 0.0273 AC: 4150 AN: 152262 Hom.: 91 Cov.: 33 AF XY: 0.0277 AC XY: 2058 AN XY: 74430

Gnomad4 AFR AF: 0.00616

Gnomad4 AMR AF: 0.0252

Gnomad4 ASJ AF: 0.0518

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0155

Gnomad4 FIN AF: 0.0381

Gnomad4 NFE AF: 0.0406

Gnomad4 OTH AF: 0.0317

Alfa AF: 0.0387 Hom.: 18

Bravo AF: 0.0252

Asia WGS AF: 0.00895 AC: 31 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	12
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243297; hg19: chr5-131999171;