rs2243297

Variant names:

• chr5-132663479-T-A
• rs2243297
• ENST00000435042.1:n.94+700A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000435042.1(TH2LCRR):​n.94+700A>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 15 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=-0.65).
• 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 the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 91 gene

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+700A>T		intron_variant	Intron 1 of 3	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

African (AFR) AF: 0.00616 AC: 256 AN: 41576

American (AMR) AF: 0.0252 AC: 385 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0518 AC: 180 AN: 3472

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5162

South Asian (SAS) AF: 0.0155 AC: 75 AN: 4826

European-Finnish (FIN) AF: 0.0381 AC: 405 AN: 10620

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0406 AC: 2761 AN: 67996

Other (OTH) AF: 0.0317 AC: 67 AN: 2114

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
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2243297; hg19: chr5-131999171;