rs3091307

Variant names:

• chr5-132653444-A-G
• rs3091307
• ENST00000458509.1:n.104+2607T>C

Variant summary

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

The ENST00000458509.1(TH2LCRR):​n.104+2607T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 152,140 control chromosomes in the GnomAD database, including 10,902 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 0.33 (10902 hom., cov: 32)
• Consequence: TH2LCRR ENST00000458509.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426
• Publications: 37 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000458509.1. 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
	TH2LCRR	NR_132125.1		n.104+2607T>C		intron	N/A
	TH2LCRR	NR_132126.1		n.174+2275T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TH2LCRR	ENST00000458509.1	TSL:1	n.104+2607T>C		intron	N/A
	TH2LCRR	ENST00000417516.2	TSL:2	n.474+2275T>C		intron	N/A
	TH2LCRR	ENST00000435042.1	TSL:5	n.94+10735T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50360 AN: 152022 Hom.: 10861 Cov.: 32

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.332 AC: 50451 AN: 152140 Hom.: 10902 Cov.: 32 AF XY: 0.329 AC XY: 24467 AN XY: 74404

African (AFR) AF: 0.624 AC: 25865 AN: 41464

American (AMR) AF: 0.211 AC: 3233 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 849 AN: 3466

East Asian (EAS) AF: 0.171 AC: 889 AN: 5188

South Asian (SAS) AF: 0.245 AC: 1184 AN: 4826

European-Finnish (FIN) AF: 0.246 AC: 2606 AN: 10596

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15017 AN: 67988

Other (OTH) AF: 0.286 AC: 605 AN: 2112

Alfa AF: 0.306 Hom.: 1062

Bravo AF: 0.342

Asia WGS AF: 0.233 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.9
DANN	Benign	0.81
PhyloP100		-0.43
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: rs3091307; hg19: chr5-131989136;