dbSNP rs7173943: ENSG00000305595:n.230-318G>C (chr15-99552246-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000811878.1(ENSG00000305595):n.230-318G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,150 control chromosomes in the GnomAD database, including 33,601 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 0.65 ( 33585 hom., cov: 30)

Exomes 𝑓: 0.37 ( 16 hom. )

Consequence

ENSG00000305595
ENST00000811878.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.486

Publications

5 publications found

Variant links:

Genes affected

ENSG00000305595 (HGNC:):

ENSG00000305595 links:

RPL7P5 (HGNC:28886): (ribosomal protein L7 pseudogene 5)

RPL7P5 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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000305595	ENST00000811878.1 link	n.230-318G>C	intron_variant	Intron 2 of 2
ENSG00000305595	ENST00000811879.1 link	n.201-318G>C	intron_variant	Intron 3 of 3
RPL7P5	ENST00000471472.2 link	n.-129C>G	upstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.649

AC:

98436

AN:

151774

Hom.:

33537

Cov.:

show subpopulations

Gnomad AFR

AF:

0.875

Gnomad AMI

AF:

0.448

Gnomad AMR

AF:

0.539

Gnomad ASJ

AF:

0.538

Gnomad EAS

AF:

0.728

Gnomad SAS

AF:

0.574

Gnomad FIN

AF:

0.601

Gnomad MID

AF:

0.598

Gnomad NFE

AF:

0.551

Gnomad OTH

AF:

0.637

GnomAD4 exome

AF:

0.372

AC:

AN:

258

Hom.:

AF XY:

0.372

AC XY:

AN XY:

164

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.417

AC:

AN:

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AF:

0.333

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.365

AC:

AN:

208

Other (OTH)

AF:

0.389

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.649

AC:

98538

AN:

151892

Hom.:

33585

Cov.:

AF XY:

0.649

AC XY:

48122

AN XY:

74184

show subpopulations

African (AFR)

AF:

0.875

AC:

36257

AN:

41438

American (AMR)

AF:

0.538

AC:

8206

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.538

AC:

1865

AN:

3466

East Asian (EAS)

AF:

0.727

AC:

3752

AN:

5158

South Asian (SAS)

AF:

0.575

AC:

2760

AN:

4804

European-Finnish (FIN)

AF:

0.601

AC:

6321

AN:

10516

Middle Eastern (MID)

AF:

0.595

AC:

175

AN:

294

European-Non Finnish (NFE)

AF:

0.551

AC:

37447

AN:

67944

Other (OTH)

AF:

0.640

AC:

1347

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1599

3198

4797

6396

7995

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

778

1556

2334

3112

3890

<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:

0.594

Hom.:

3517

Bravo

AF:

0.657

Asia WGS

AF:

0.655

AC:

2277

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.1

(source)

DANN

Benign

0.64

PhyloP100

-0.49

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