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

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000503179.6(MRPS30-DT):​n.162-9452G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRPS30-DT	NR_109862.1	n.153-10343G>T		intron_variant	Intron 1 of 3
MRPS30-DT	NR_109863.1	n.153-10343G>T		intron_variant	Intron 1 of 3
MRPS30-DT	NR_109864.1	n.152+21198G>T		intron_variant	Intron 1 of 2
MRPS30-DT	NR_109865.1	n.152+21198G>T		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>T		intron_variant	Intron 1 of 2	4
MRPS30-DT	ENST00000503452.6	n.136+21198G>T		intron_variant	Intron 1 of 2	2
MRPS30-DT	ENST00000505302.2	n.148+21198G>T		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 21

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.31
PhyloP100		-1.4

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;