Genetic Variant PP12613:n.1752G>T (chr4-121766336-G-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The ENST00000424958.2(PP12613):n.1752G>T variant causes a non coding transcript exon 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: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

PP12613
ENST00000424958.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.320

Publications

11 publications found

Variant links:

Genes affected

PP12613 (HGNC:):

PP12613 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (REVEL=0.038).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PP12613	NR_024365.1 link	n.1752G>T		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PP12613	ENST00000424958.2 link	n.1752G>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
PP12613	ENST00000746424.1 link	n.240+917G>T	intron_variant	Intron 1 of 1
PP12613	ENST00000746425.1 link	n.238+917G>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

301694

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

171926

African (AFR)

AF:

0.00

AC:

AN:

8554

American (AMR)

AF:

0.00

AC:

AN:

27266

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

10750

East Asian (EAS)

AF:

0.00

AC:

AN:

9202

South Asian (SAS)

AF:

0.00

AC:

AN:

59586

European-Finnish (FIN)

AF:

0.00

AC:

AN:

12348

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1402

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

158542

Other (OTH)

AF:

0.00

AC:

AN:

14044

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

3699

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.0

(source)

DANN

Benign

0.26

PhyloP100

-0.32

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

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over