Genetic Variant MRPS30-DT:n.258-8495A>G (chr5-44512967-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000671607.2(MRPS30-DT):n.258-8495A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0631 in 152,116 control chromosomes in the GnomAD database, including 368 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 0.063 ( 368 hom., cov: 32)

Consequence

MRPS30-DT
ENST00000671607.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0360

Variant links:

Genes affected

MRPS30-DT (HGNC:53420): (MRPS30 divergent transcript)

MRPS30-DT 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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.07 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
MRPS30-DT	ENST00000671607.2 link	n.258-8495A>G	intron_variant	Intron 2 of 4
MRPS30-DT	ENST00000715752.1 link	n.1089-8495A>G	intron_variant	Intron 4 of 6
MRPS30-DT	ENST00000715753.1 link	n.704-2879A>G	intron_variant	Intron 5 of 8

Frequencies

GnomAD3 genomes

AF:

0.0631

AC:

9589

AN:

151998

Hom.:

367

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0612

Gnomad AMI

AF:

0.0581

Gnomad AMR

AF:

0.0660

Gnomad ASJ

AF:

0.0767

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0203

Gnomad FIN

AF:

0.0559

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0716

Gnomad OTH

AF:

0.0689

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

GnomAD4 genome

AF:

0.0631

AC:

9596

AN:

152116

Hom.:

368

Cov.:

AF XY:

0.0622

AC XY:

4622

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.0612

AC:

2542

AN:

41514

American (AMR)

AF:

0.0659

AC:

1004

AN:

15242

Ashkenazi Jewish (ASJ)

AF:

0.0767

AC:

266

AN:

3470

East Asian (EAS)

AF:

0.00116

AC:

AN:

5174

South Asian (SAS)

AF:

0.0203

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.0559

AC:

592

AN:

10596

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0717

AC:

4871

AN:

67980

Other (OTH)

AF:

0.0677

AC:

143

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

466

932

1398

1864

2330

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0681

Hom.:

223

Bravo

AF:

0.0633

Asia WGS

AF:

0.0160

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.6

(source)

DANN

Benign

0.61

PhyloP100

-0.036

Splicing

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

Publications

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chr5-44512967-T-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over