rs12474719

Variant names:

• chr2-216759000-G-A
• rs12474719
• ENST00000447289.1:n.389-5889G>A

Variant summary

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

The NR_187138.1(IGFBP-AS1):​n.407-5889G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,114 control chromosomes in the GnomAD database, including 2,947 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 0.18 (2947 hom., cov: 32)
• Consequence: IGFBP-AS1 NR_187138.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 6 publications found

Genes affected

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

IGFBP-AS1 (HGNC:55655): (IGFBP5 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_187138.1. 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
	IGFBP-AS1	NR_187138.1		n.407-5889G>A		intron	N/A
	IGFBP-AS1	NR_187139.1		n.407-5889G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TESHL	ENST00000447289.1	TSL:5	n.389-5889G>A		intron	N/A
	TESHL	ENST00000695932.1		n.448+46531G>A		intron	N/A
	TESHL	ENST00000695934.1		n.111+46531G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27624 AN: 151996 Hom.: 2935 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.182 AC: 27666 AN: 152114 Hom.: 2947 Cov.: 32 AF XY: 0.184 AC XY: 13680 AN XY: 74358

African (AFR) AF: 0.279 AC: 11574 AN: 41480

American (AMR) AF: 0.223 AC: 3411 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 631 AN: 3472

East Asian (EAS) AF: 0.292 AC: 1506 AN: 5154

South Asian (SAS) AF: 0.161 AC: 779 AN: 4824

European-Finnish (FIN) AF: 0.120 AC: 1266 AN: 10588

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7906 AN: 67998

Other (OTH) AF: 0.172 AC: 363 AN: 2108

Alfa AF: 0.164 Hom.: 488

Bravo AF: 0.195

Asia WGS AF: 0.210 AC: 732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.46
DANN	Benign	0.68
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs12474719; hg19: chr2-217623723;