rs2069757

Variant names:

• chr5-132662721-G-A
• rs2069757
• ENST00000435042.1:n.94+1458C>T

Variant summary

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

The ENST00000435042.1(TH2LCRR):​n.94+1458C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0774 in 152,266 control chromosomes in the GnomAD database, including 573 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 0.077 (573 hom., cov: 33)
• Consequence: TH2LCRR ENST00000435042.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

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+1458C>T		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.0774 AC: 11782 AN: 152148 Hom.: 574 Cov.: 33

Gnomad AFR AF: 0.0375

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0711

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0821

Gnomad OTH AF: 0.0914

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

GnomAD4 genome AF: 0.0774 AC: 11778 AN: 152266 Hom.: 573 Cov.: 33 AF XY: 0.0795 AC XY: 5917 AN XY: 74454

Gnomad4 AFR AF: 0.0373

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.0711

Gnomad4 NFE AF: 0.0821

Gnomad4 OTH AF: 0.0895

Alfa AF: 0.0859 Hom.: 145

Bravo AF: 0.0795

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2069757; hg19: chr5-131998413;