Genetic Variant RN7SL388P:n.108C>A (chrX-72198819-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000498736.3(RN7SL388P):n.108C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 109,338 control chromosomes in the GnomAD database, including 8,964 homozygotes. There are 13,324 hemizygotes in GnomAD. 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 0.42 ( 8964 hom., 13316 hem., cov: 21)

Exomes 𝑓: 0.22 ( 0 hom. 8 hem. )

Consequence

RN7SL388P
ENST00000498736.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.546

Publications

2 publications found

Variant links:

Genes affected

RN7SL388P (HGNC:46404): (RNA, 7SL, cytoplasmic 388, pseudogene)

RN7SL388P links:

PIN4 (HGNC:8992): (peptidylprolyl cis/trans isomerase, NIMA-interacting 4) This gene encodes a member of the parvulin subfamily of the peptidyl-prolyl cis/trans isomerase protein family. The encoded protein catalyzes the isomerization of peptidylprolyl bonds, and may play a role in the cell cycle, chromatin remodeling, and/or ribosome biogenesis. The encoded protein may play an additional role in the mitochondria. [provided by RefSeq, Dec 2009]

PIN4 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RN7SL388P		n.72198819C>A		intragenic_variant
PIN4	NM_001170747.1 link	c.312+1915C>A		intron_variant	Intron 3 of 3		NP_001164218.1	Q9Y237-3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
RN7SL388P	ENST00000498736.3 link	n.108C>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
PIN4	ENST00000423432.6 link	c.312+1915C>A	intron_variant	Intron 3 of 3	2	ENSP00000409154.2	Q9Y237-3
PIN4	ENST00000652108.2 link	c.264+1915C>A	intron_variant	Intron 3 of 3		ENSP00000498324.2	A0A494C021

Frequencies

GnomAD3 genomes

AF:

0.424

AC:

46341

AN:

109237

Hom.:

8966

Cov.:

show subpopulations

Gnomad AFR

AF:

0.693

Gnomad AMI

AF:

0.315

Gnomad AMR

AF:

0.416

Gnomad ASJ

AF:

0.296

Gnomad EAS

AF:

0.983

Gnomad SAS

AF:

0.655

Gnomad FIN

AF:

0.264

Gnomad MID

AF:

0.300

Gnomad NFE

AF:

0.252

Gnomad OTH

AF:

0.380

GnomAD4 exome

AF:

0.216

AC:

AN:

Hom.:

Cov.:

AF XY:

0.421

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.191

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.424

AC:

46382

AN:

109287

Hom.:

8964

Cov.:

AF XY:

0.421

AC XY:

13316

AN XY:

31641

show subpopulations

African (AFR)

AF:

0.694

AC:

20725

AN:

29882

American (AMR)

AF:

0.416

AC:

4248

AN:

10220

Ashkenazi Jewish (ASJ)

AF:

0.296

AC:

775

AN:

2616

East Asian (EAS)

AF:

0.983

AC:

3385

AN:

3444

South Asian (SAS)

AF:

0.653

AC:

1616

AN:

2473

European-Finnish (FIN)

AF:

0.264

AC:

1528

AN:

5793

Middle Eastern (MID)

AF:

0.325

AC:

AN:

212

European-Non Finnish (NFE)

AF:

0.252

AC:

13253

AN:

52492

Other (OTH)

AF:

0.385

AC:

572

AN:

1486

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

780

1559

2339

3118

3898

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

428

856

1284

1712

2140

<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:

0.343

Hom.:

2337

Bravo

AF:

0.451

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.1

(source)

DANN

Benign

0.85

PhyloP100

-0.55

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over