chr2-217006626-A-G

Variant names:

• chr2-217006626-A-G
• rs10169372
• ENST00000695932.1:n.509+12608A>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+12608A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0766 in 152,102 control chromosomes in the GnomAD database, including 1,218 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 0.077 (1218 hom., cov: 32)
• Consequence: TESHL ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762
• Publications: 3 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TESHL	ENST00000695932.1		n.509+12608A>G		intron	N/A
	TESHL	ENST00000695934.1		n.172+12608A>G		intron	N/A
	TESHL	ENST00000695937.1		n.221+12608A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0764 AC: 11619 AN: 151984 Hom.: 1216 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0341

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.0386

Gnomad SAS AF: 0.0510

Gnomad FIN AF: 0.00151

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.00694

Gnomad OTH AF: 0.0586

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

GnomAD4 genome AF: 0.0766 AC: 11650 AN: 152102 Hom.: 1218 Cov.: 32 AF XY: 0.0744 AC XY: 5529 AN XY: 74354

African (AFR) AF: 0.240 AC: 9956 AN: 41430

American (AMR) AF: 0.0340 AC: 520 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0303 AC: 105 AN: 3470

East Asian (EAS) AF: 0.0383 AC: 198 AN: 5168

South Asian (SAS) AF: 0.0507 AC: 244 AN: 4816

European-Finnish (FIN) AF: 0.00151 AC: 16 AN: 10608

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.00694 AC: 472 AN: 68020

Other (OTH) AF: 0.0570 AC: 120 AN: 2104

Alfa AF: 0.0352 Hom.: 153

Bravo AF: 0.0859

Asia WGS AF: 0.0510 AC: 178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.2
DANN	Benign	0.60
PhyloP100		0.76

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10169372;

hg19: chr2-217871349;