5-44805824-A-G

Variant names:

• chr5-44805824-A-G
• rs13159598
• ENST00000503179.5:n.118+2818T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000503452.5(MRPS30-DT):​n.136+2818T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 152,004 control chromosomes in the GnomAD database, including 16,015 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 0.45 (16015 hom., cov: 32)
• Consequence: MRPS30-DT ENST00000503452.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.455

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRPS30-DT	NR_109862.1	n.152+2818T>C		intron_variant	Intron 1 of 3
MRPS30-DT	NR_109863.1	n.152+2818T>C		intron_variant	Intron 1 of 3
MRPS30-DT	NR_109864.1	n.152+2818T>C		intron_variant	Intron 1 of 2
MRPS30-DT	NR_109865.1	n.152+2818T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRPS30-DT	ENST00000503179.5	n.118+2818T>C		intron_variant	Intron 1 of 2	4
MRPS30-DT	ENST00000503452.5	n.136+2818T>C		intron_variant	Intron 1 of 2	2
MRPS30-DT	ENST00000505302.1	n.100+2818T>C		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68718 AN: 151886 Hom.: 15972 Cov.: 32

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.453 AC: 68811 AN: 152004 Hom.: 16015 Cov.: 32 AF XY: 0.456 AC XY: 33854 AN XY: 74298

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.453

Alfa AF: 0.420 Hom.: 7530

Bravo AF: 0.461

Asia WGS AF: 0.561 AC: 1947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.4
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13159598; hg19: chr5-44805926;