rs2330572

Variant names:

• chr5-44740887-A-C
• rs2330572
• ENST00000671607.2:n.161+67755T>G

Variant summary

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

The ENST00000671607.2(MRPS30-DT):​n.161+67755T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 151,828 control chromosomes in the GnomAD database, including 16,885 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 0.46 (16885 hom., cov: 32)
• Consequence: MRPS30-DT ENST00000671607.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591
• Publications: 11 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRPS30-DT	ENST00000671607.2	n.161+67755T>G		intron_variant	Intron 1 of 4
MRPS30-DT	ENST00000715752.1	n.411+4324T>G		intron_variant	Intron 3 of 6
MRPS30-DT	ENST00000715753.1	n.412+4324T>G		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70420 AN: 151708 Hom.: 16842 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.464 AC: 70516 AN: 151828 Hom.: 16885 Cov.: 32 AF XY: 0.467 AC XY: 34629 AN XY: 74162

African (AFR) AF: 0.558 AC: 23130 AN: 41432

American (AMR) AF: 0.475 AC: 7231 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1500 AN: 3470

East Asian (EAS) AF: 0.556 AC: 2844 AN: 5116

South Asian (SAS) AF: 0.485 AC: 2339 AN: 4822

European-Finnish (FIN) AF: 0.399 AC: 4205 AN: 10550

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27869 AN: 67900

Other (OTH) AF: 0.459 AC: 966 AN: 2106

Alfa AF: 0.427 Hom.: 12860

Bravo AF: 0.475

Asia WGS AF: 0.561 AC: 1945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.59
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs2330572; hg19: chr5-44740989;