dbSNP rs7622210: RPL7P16:n.132243465A>G (chr3-132243465-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The variant allele was found at a frequency of 0.154 in 270,668 control chromosomes in the GnomAD database, including 3,904 homozygotes. 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 0.17 ( 2813 hom., cov: 33)

Exomes 𝑓: 0.13 ( 1091 hom. )

Consequence

RPL7P16
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.27

Publications

5 publications found

Variant links:

Genes affected

RPL7P16 (HGNC:36591): (ribosomal protein L7 pseudogene 16)

RPL7P16 links:

CPNE4 (HGNC:2317): (copine 4) This gene belongs to the highly conserved copine family. It encodes a calcium-dependent, phospholipid-binding protein, which may be involved in membrane trafficking, mitogenesis and development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

CPNE4 links:

Genome browser will be placed here

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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL7P16		n.132243465A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPNE4	ENST00000512055.5 link	c.-1829+40578T>C		intron_variant	Intron 2 of 19	2		ENSP00000421705.1		Q96A23-1
RPL7P16	ENST00000479738.1 link	n.*63T>C		downstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26404

AN:

152034

Hom.:

2800

Cov.:

show subpopulations

Gnomad AFR

AF:

0.305

Gnomad AMI

AF:

0.144

Gnomad AMR

AF:

0.106

Gnomad ASJ

AF:

0.0880

Gnomad EAS

AF:

0.168

Gnomad SAS

AF:

0.106

Gnomad FIN

AF:

0.161

Gnomad MID

AF:

0.0828

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.162

GnomAD4 exome

AF:

0.130

AC:

15353

AN:

118516

Hom.:

1091

AF XY:

0.129

AC XY:

8487

AN XY:

66014

show subpopulations

African (AFR)

AF:

0.324

AC:

808

AN:

2490

American (AMR)

AF:

0.0858

AC:

411

AN:

4790

Ashkenazi Jewish (ASJ)

AF:

0.0952

AC:

285

AN:

2994

East Asian (EAS)

AF:

0.195

AC:

909

AN:

4658

South Asian (SAS)

AF:

0.116

AC:

2162

AN:

18686

European-Finnish (FIN)

AF:

0.147

AC:

840

AN:

5724

Middle Eastern (MID)

AF:

0.100

AC:

AN:

510

European-Non Finnish (NFE)

AF:

0.125

AC:

9001

AN:

72010

Other (OTH)

AF:

0.133

AC:

886

AN:

6654

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

632

1263

1895

2526

3158

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

180

240

300

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.174

AC:

26447

AN:

152152

Hom.:

2813

Cov.:

AF XY:

0.173

AC XY:

12843

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.305

AC:

12652

AN:

41480

American (AMR)

AF:

0.106

AC:

1622

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0880

AC:

305

AN:

3466

East Asian (EAS)

AF:

0.167

AC:

863

AN:

5170

South Asian (SAS)

AF:

0.107

AC:

516

AN:

4824

European-Finnish (FIN)

AF:

0.161

AC:

1709

AN:

10588

Middle Eastern (MID)

AF:

0.0788

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.122

AC:

8283

AN:

68012

Other (OTH)

AF:

0.162

AC:

343

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1094

2188

3283

4377

5471

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

276

552

828

1104

1380

<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:

0.135

Hom.:

782

Bravo

AF:

0.176

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.26

(source)

DANN

Benign

0.75

PhyloP100

-1.3

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over