rs11695415

Variant names:

• chr2-217273761-T-C
• rs11695415
• ENST00000655995.2:n.420-3837T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-217273761-T-C
• chr2-217273761-T-G

Variant summary

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

The ENST00000655995.2(TESHL):​n.420-3837T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 151,888 control chromosomes in the GnomAD database, including 2,709 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 0.19 (2709 hom., cov: 31)
• Consequence: TESHL ENST00000655995.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132
• Publications: 8 publications found

Genes affected

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

ENSG00000297094 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.285 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
TESHL	ENST00000655995.2	n.420-3837T>C		intron_variant	Intron 4 of 8
TESHL	ENST00000657920.1	n.420-3837T>C		intron_variant	Intron 4 of 8
TESHL	ENST00000695932.1	n.854-3837T>C		intron_variant	Intron 6 of 11
ENSG00000297094	ENST00000745361.1	n.158-5297A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28186 AN: 151770 Hom.: 2708 Cov.: 31

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.186 AC: 28201 AN: 151888 Hom.: 2709 Cov.: 31 AF XY: 0.189 AC XY: 14042 AN XY: 74228

African (AFR) AF: 0.211 AC: 8759 AN: 41418

American (AMR) AF: 0.193 AC: 2950 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 497 AN: 3470

East Asian (EAS) AF: 0.297 AC: 1532 AN: 5154

South Asian (SAS) AF: 0.145 AC: 697 AN: 4818

European-Finnish (FIN) AF: 0.239 AC: 2505 AN: 10500

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10525 AN: 67950

Other (OTH) AF: 0.196 AC: 413 AN: 2110

Alfa AF: 0.175 Hom.: 416

Bravo AF: 0.183

Asia WGS AF: 0.256 AC: 889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.63
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs11695415; hg19: chr2-218138484;