2-216998758-C-G

Variant names:

• chr2-216998758-C-G
• rs10932688
• ENST00000695932.1:n.509+4740C>G

Variant summary

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

The ENST00000695932.1(TESHL):​n.509+4740C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,064 control chromosomes in the GnomAD database, including 6,615 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 0.25 (6615 hom., cov: 32)
• Consequence: TESHL ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 13 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 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	ENST00000695932.1	n.509+4740C>G		intron_variant	Intron 3 of 11
TESHL	ENST00000695934.1	n.172+4740C>G		intron_variant	Intron 3 of 8
TESHL	ENST00000695937.1	n.221+4740C>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38447 AN: 151946 Hom.: 6604 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.253 AC: 38474 AN: 152064 Hom.: 6615 Cov.: 32 AF XY: 0.261 AC XY: 19368 AN XY: 74326

African (AFR) AF: 0.101 AC: 4197 AN: 41522

American (AMR) AF: 0.391 AC: 5978 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 550 AN: 3470

East Asian (EAS) AF: 0.834 AC: 4307 AN: 5166

South Asian (SAS) AF: 0.276 AC: 1325 AN: 4802

European-Finnish (FIN) AF: 0.336 AC: 3550 AN: 10556

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17808 AN: 67958

Other (OTH) AF: 0.258 AC: 544 AN: 2112

Alfa AF: 0.145 Hom.: 305

Bravo AF: 0.257

Asia WGS AF: 0.559 AC: 1939 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	1.1
DANN	Benign	0.49
PhyloP100		-0.014

Splicing

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

Other links and lift over

dbSNP: rs10932688; hg19: chr2-217863481;