Genetic Variant PNCRNA-D:n.435delC (chr11-69639561-AC-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000754571.1(PNCRNA-D):n.435delC variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.57 ( 22287 hom., cov: 0)

Consequence

PNCRNA-D
ENST00000754571.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.952

Publications

2 publications found

Variant links:

Genes affected

PNCRNA-D (HGNC:58269):

PNCRNA-D links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000754571.1. 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
	PNCRNA-D	ENST00000754571.1		n.435delC		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.567

AC:

79801

AN:

140620

Hom.:

22254

Cov.:

show subpopulations

Gnomad AFR

AF:

0.615

Gnomad AMI

AF:

0.464

Gnomad AMR

AF:

0.541

Gnomad ASJ

AF:

0.578

Gnomad EAS

AF:

0.841

Gnomad SAS

AF:

0.714

Gnomad FIN

AF:

0.513

Gnomad MID

AF:

0.577

Gnomad NFE

AF:

0.523

Gnomad OTH

AF:

0.601

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

GnomAD4 genome

AF:

0.568

AC:

79867

AN:

140702

Hom.:

22287

Cov.:

AF XY:

0.576

AC XY:

39056

AN XY:

67794

show subpopulations

African (AFR)

AF:

0.615

AC:

23041

AN:

37456

American (AMR)

AF:

0.540

AC:

7280

AN:

13470

Ashkenazi Jewish (ASJ)

AF:

0.578

AC:

1963

AN:

3398

East Asian (EAS)

AF:

0.841

AC:

3957

AN:

4704

South Asian (SAS)

AF:

0.715

AC:

3170

AN:

4434

European-Finnish (FIN)

AF:

0.513

AC:

4301

AN:

8384

Middle Eastern (MID)

AF:

0.579

AC:

162

AN:

280

European-Non Finnish (NFE)

AF:

0.523

AC:

34413

AN:

65758

Other (OTH)

AF:

0.605

AC:

1170

AN:

1934

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1669

3339

5008

6678

8347

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

702

1404

2106

2808

3510

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.316

Hom.:

558

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.95

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over