rs3091307

Positions:

• chr5-132653444-A-G

Variant summary

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

The ENST00000435042.1(TH2LCRR):​n.94+10735T>C 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 0.332 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 ENST00000435042.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TH2LCRR	NR_132125.1	n.104+2607T>C		intron_variant, non_coding_transcript_variant
TH2LCRR	NR_132126.1	n.174+2275T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TH2LCRR	ENST00000435042.1	n.94+10735T>C		intron_variant, non_coding_transcript_variant		5
TH2LCRR	ENST00000458509.1	n.104+2607T>C		intron_variant, non_coding_transcript_variant		1
TH2LCRR	ENST00000417516.1	n.174+2275T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.286

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.9
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3091307; hg19: chr5-131989136;