ENST00000503179.6:n.162-9452G>A

Variant names:

• chr5-44787444-C-T
• rs2118763
• ENST00000503179.6:n.162-9452G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000503179.6(MRPS30-DT):​n.162-9452G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0228 in 152,176 control chromosomes in the GnomAD database, including 82 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 0.023 (82 hom., cov: 33)
• Consequence: MRPS30-DT ENST00000503179.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRPS30-DT	NR_109862.1	n.153-10343G>A		intron_variant	Intron 1 of 3
MRPS30-DT	NR_109863.1	n.153-10343G>A		intron_variant	Intron 1 of 3
MRPS30-DT	NR_109864.1	n.152+21198G>A		intron_variant	Intron 1 of 2
MRPS30-DT	NR_109865.1	n.152+21198G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRPS30-DT	ENST00000503179.6	n.162-9452G>A		intron_variant	Intron 1 of 2	4
MRPS30-DT	ENST00000503452.6	n.136+21198G>A		intron_variant	Intron 1 of 2	2
MRPS30-DT	ENST00000505302.2	n.148+21198G>A		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.0228 AC: 3474 AN: 152056 Hom.: 85 Cov.: 33

Gnomad AFR AF: 0.00553

Gnomad AMI AF: 0.0176

Gnomad AMR AF: 0.0366

Gnomad ASJ AF: 0.00750

Gnomad EAS AF: 0.0576

Gnomad SAS AF: 0.0775

Gnomad FIN AF: 0.0223

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0249

Gnomad OTH AF: 0.0172

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

GnomAD4 genome AF: 0.0228 AC: 3468 AN: 152176 Hom.: 82 Cov.: 33 AF XY: 0.0239 AC XY: 1782 AN XY: 74408

African (AFR) AF: 0.00551 AC: 229 AN: 41540

American (AMR) AF: 0.0365 AC: 558 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00750 AC: 26 AN: 3468

East Asian (EAS) AF: 0.0577 AC: 299 AN: 5178

South Asian (SAS) AF: 0.0763 AC: 368 AN: 4820

European-Finnish (FIN) AF: 0.0223 AC: 236 AN: 10604

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0249 AC: 1693 AN: 67974

Other (OTH) AF: 0.0175 AC: 37 AN: 2112

Alfa AF: 0.0214 Hom.: 21

Bravo AF: 0.0241

Asia WGS AF: 0.0830 AC: 288 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.46
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2118763; hg19: chr5-44787546;