Genetic Variant ENST00000388955.8:n.703+235G>A (chr7-72951917-C-T) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000388955.8(NSUN5P2):n.703+235G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.36 ( 7469 hom., cov: 0)

Failed GnomAD Quality Control

Consequence

NSUN5P2
ENST00000388955.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.14

Publications

1 publications found

Variant links:

COSMIC-nc: COSV57512925

Genes affected

NSUN5P2 (HGNC:):

NSUN5P2 links:

NSUN5P2 (HGNC:16609): (NSUN5 pseudogene 2) This locus represents a transcribed pseudogene of a nearby locus on chromosome 7, which encodes a putative methyltransferase. There is also a third closely related pseudogene locus in this region. There is extensive alternative splicing at this locus. [provided by RefSeq, Jul 2013]

NSUN5P2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.03).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NSUN5P2	NR_033323.3 link	n.676+235G>A		intron_variant	Intron 5 of 10

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
NSUN5P2	ENST00000388955.8 link	n.703+235G>A	intron_variant	Intron 5 of 10	1
NSUN5P2	ENST00000444583.7 link	n.121-1721G>A	intron_variant	Intron 1 of 6	1
NSUN5P2	ENST00000485741.6 link	n.633+235G>A	intron_variant	Intron 5 of 11	1

Frequencies

GnomAD3 genomes

AF:

0.363

AC:

20522

AN:

56498

Hom.:

7457

Cov.:

show subpopulations

Gnomad AFR

AF:

0.347

Gnomad AMI

AF:

0.529

Gnomad AMR

AF:

0.306

Gnomad ASJ

AF:

0.268

Gnomad EAS

AF:

0.410

Gnomad SAS

AF:

0.350

Gnomad FIN

AF:

0.353

Gnomad MID

AF:

0.357

Gnomad NFE

AF:

0.378

Gnomad OTH

AF:

0.338

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

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.364

AC:

20546

AN:

56506

Hom.:

7469

Cov.:

AF XY:

0.361

AC XY:

9650

AN XY:

26746

show subpopulations

African (AFR)

AF:

0.347

AC:

1465

AN:

4218

American (AMR)

AF:

0.307

AC:

1669

AN:

5440

Ashkenazi Jewish (ASJ)

AF:

0.268

AC:

488

AN:

1818

East Asian (EAS)

AF:

0.408

AC:

181

AN:

444

South Asian (SAS)

AF:

0.352

AC:

591

AN:

1678

European-Finnish (FIN)

AF:

0.353

AC:

1613

AN:

4570

Middle Eastern (MID)

AF:

0.377

AC:

AN:

138

European-Non Finnish (NFE)

AF:

0.378

AC:

13934

AN:

36852

Other (OTH)

AF:

0.351

AC:

317

AN:

902

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

192

384

576

768

960

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

158

316

474

632

790

<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:

0.337

Hom.:

1006

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.0

(source)

DANN

Benign

0.72

PhyloP100

-2.1

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over