ENST00000695932.1:n.509+131991T>C

Variant names:

• chr2-217126009-T-C
• rs10498054
• ENST00000695932.1:n.509+131991T>C

Variant summary

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

The ENST00000695932.1(TESHL):​n.509+131991T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0309 in 152,254 control chromosomes in the GnomAD database, including 145 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 0.031 (145 hom., cov: 32)
• Consequence: TESHL ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0888 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000695932.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TESHL	ENST00000695932.1		n.509+131991T>C		intron	N/A
	TESHL	ENST00000695934.1		n.173-27402T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0309 AC: 4700 AN: 152136 Hom.: 144 Cov.: 32

Gnomad AFR AF: 0.0432

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0929

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.00501

Gnomad SAS AF: 0.0626

Gnomad FIN AF: 0.00358

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0146

Gnomad OTH AF: 0.0297

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

GnomAD4 genome AF: 0.0309 AC: 4709 AN: 152254 Hom.: 145 Cov.: 32 AF XY: 0.0318 AC XY: 2365 AN XY: 74438

African (AFR) AF: 0.0432 AC: 1796 AN: 41548

American (AMR) AF: 0.0929 AC: 1419 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0179 AC: 62 AN: 3472

East Asian (EAS) AF: 0.00502 AC: 26 AN: 5180

South Asian (SAS) AF: 0.0629 AC: 303 AN: 4820

European-Finnish (FIN) AF: 0.00358 AC: 38 AN: 10622

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0146 AC: 996 AN: 68014

Other (OTH) AF: 0.0298 AC: 63 AN: 2112

Alfa AF: 0.0272 Hom.: 9

Bravo AF: 0.0382

Asia WGS AF: 0.0480 AC: 165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.68
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs10498054; hg19: chr2-217990732;