chr2-216760956-G-A

Variant names:

• chr2-216760956-G-A
• rs13020935
• ENST00000447289.1:n.389-3933G>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.407-3933G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 152,014 control chromosomes in the GnomAD database, including 32,410 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 0.64 (32410 hom., cov: 32)
• Consequence: IGFBP-AS1 NR_187138.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.426
• Publications: 5 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.728 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IGFBP-AS1	NR_187138.1		n.407-3933G>A		intron	N/A
	IGFBP-AS1	NR_187139.1		n.407-3933G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TESHL	ENST00000447289.1	TSL:5	n.389-3933G>A		intron	N/A
	TESHL	ENST00000695932.1		n.448+48487G>A		intron	N/A
	TESHL	ENST00000695934.1		n.111+48487G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.645 AC: 97974 AN: 151896 Hom.: 32390 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.645 AC: 98029 AN: 152014 Hom.: 32410 Cov.: 32 AF XY: 0.640 AC XY: 47556 AN XY: 74284

African (AFR) AF: 0.508 AC: 21072 AN: 41446

American (AMR) AF: 0.621 AC: 9488 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2632 AN: 3470

East Asian (EAS) AF: 0.522 AC: 2694 AN: 5162

South Asian (SAS) AF: 0.705 AC: 3389 AN: 4808

European-Finnish (FIN) AF: 0.627 AC: 6606 AN: 10544

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.733 AC: 49839 AN: 67978

Other (OTH) AF: 0.688 AC: 1455 AN: 2116

Alfa AF: 0.701 Hom.: 21107

Bravo AF: 0.643

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.1
DANN	Benign	0.75
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs13020935; hg19: chr2-217625679;