rs13153459

Variant names:

• chr5-44515833-A-C
• rs13153459
• ENST00000671607.2:n.258-11361T>G

Your query was ambiguous. Multiple possible variants found:

• chr5-44515833-A-C
• chr5-44515833-A-T

Variant summary

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

The ENST00000671607.2(MRPS30-DT):​n.258-11361T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 151,790 control chromosomes in the GnomAD database, including 4,799 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 0.24 (4799 hom., cov: 31)
• Consequence: MRPS30-DT ENST00000671607.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.791
• Publications: 7 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671607.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRPS30-DT	ENST00000671607.2		n.258-11361T>G		intron	N/A
	MRPS30-DT	ENST00000715752.1		n.1089-11361T>G		intron	N/A
	MRPS30-DT	ENST00000715753.1		n.704-5745T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36003 AN: 151672 Hom.: 4786 Cov.: 31

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.237 AC: 36035 AN: 151790 Hom.: 4799 Cov.: 31 AF XY: 0.236 AC XY: 17536 AN XY: 74182

African (AFR) AF: 0.359 AC: 14849 AN: 41336

American (AMR) AF: 0.201 AC: 3059 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1071 AN: 3464

East Asian (EAS) AF: 0.129 AC: 664 AN: 5150

South Asian (SAS) AF: 0.140 AC: 672 AN: 4814

European-Finnish (FIN) AF: 0.181 AC: 1920 AN: 10586

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13129 AN: 67916

Other (OTH) AF: 0.228 AC: 479 AN: 2098

Alfa AF: 0.195 Hom.: 2646

Bravo AF: 0.247

Asia WGS AF: 0.155 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.1
DANN	Benign	0.65
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs13153459; hg19: chr5-44515935;