Genetic Variant TESHL:n.394+7964A>T (chr2-217310749-A-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000474063.5(DIRC3):n.2233+7217T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)

Consequence

DIRC3
ENST00000474063.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.887

Publications

5 publications found

Variant links:

Genes affected

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

TESHL links:

DIRC3 (HGNC:17805): (disrupted in renal carcinoma 3)

DIRC3 links:

DIRC3-AS1 (HGNC:50636): (DIRC3 antisense RNA 1)

DIRC3-AS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000474063.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
DIRC3	NR_026597.2	n.3065+7217T>A	intron	N/A
DIRC3-AS1	NR_133642.1	n.400+7964A>T	intron	N/A
DIRC3	NR_186292.1	n.4304+7217T>A	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
TESHL	ENST00000452813.1	TSL:3	n.394+7964A>T	intron	N/A
DIRC3	ENST00000474063.5	TSL:2	n.2233+7217T>A	intron	N/A
DIRC3	ENST00000486365.6	TSL:5	n.3065+7217T>A	intron	N/A

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

185677

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.059

(source)

DANN

Benign

0.34

PhyloP100

-0.89

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over