rs1882420

Variant names:

• chr2-216986786-G-T
• rs1882420
• ENST00000447289.1:n.511-7172G>T

Variant summary

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

The ENST00000607591.1(TESHL):​n.272+4657G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,046 control chromosomes in the GnomAD database, including 11,291 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 0.30 (11291 hom., cov: 32)
• Consequence: TESHL ENST00000607591.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 3 publications found

Genes affected

TESHL (HGNC:52740): (testicular germ cell expressed HSF2 interacting lncRNA)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607591.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TESHL	ENST00000447289.1	TSL:5	n.511-7172G>T		intron	N/A
	TESHL	ENST00000607591.1	TSL:3	n.272+4657G>T		intron	N/A
	TESHL	ENST00000695932.1		n.449-7172G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45352 AN: 151928 Hom.: 11249 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.299 AC: 45453 AN: 152046 Hom.: 11291 Cov.: 32 AF XY: 0.300 AC XY: 22262 AN XY: 74312

African (AFR) AF: 0.680 AC: 28155 AN: 41424

American (AMR) AF: 0.263 AC: 4026 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 391 AN: 3472

East Asian (EAS) AF: 0.148 AC: 764 AN: 5176

South Asian (SAS) AF: 0.142 AC: 684 AN: 4808

European-Finnish (FIN) AF: 0.210 AC: 2221 AN: 10564

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8400 AN: 68004

Other (OTH) AF: 0.254 AC: 536 AN: 2114

Alfa AF: 0.162 Hom.: 6246

Bravo AF: 0.322

Asia WGS AF: 0.181 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.13
DANN	Benign	0.66
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1882420; hg19: chr2-217851509;