rs13169538

Variant names:

• chr5-44569938-G-A
• rs13169538
• ENST00000671607.2:n.258-65466C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-44569938-G-A
• chr5-44569938-G-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.258-65466C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0778 in 151,942 control chromosomes in the GnomAD database, including 565 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 0.078 (565 hom., cov: 32)
• Consequence: MRPS30-DT ENST00000671607.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRPS30-DT	ENST00000671607.2		n.258-65466C>T		intron	N/A
	MRPS30-DT	ENST00000715752.1		n.1089-65466C>T		intron	N/A
	MRPS30-DT	ENST00000715753.1		n.704-59850C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0778 AC: 11808 AN: 151824 Hom.: 561 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0679

Gnomad ASJ AF: 0.0832

Gnomad EAS AF: 0.00600

Gnomad SAS AF: 0.0211

Gnomad FIN AF: 0.0563

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0715

Gnomad OTH AF: 0.0786

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

GnomAD4 genome AF: 0.0778 AC: 11824 AN: 151942 Hom.: 565 Cov.: 32 AF XY: 0.0761 AC XY: 5651 AN XY: 74270

African (AFR) AF: 0.113 AC: 4684 AN: 41498

American (AMR) AF: 0.0678 AC: 1031 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.0832 AC: 288 AN: 3462

East Asian (EAS) AF: 0.00601 AC: 31 AN: 5156

South Asian (SAS) AF: 0.0211 AC: 102 AN: 4826

European-Finnish (FIN) AF: 0.0563 AC: 596 AN: 10590

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0715 AC: 4855 AN: 67882

Other (OTH) AF: 0.0778 AC: 164 AN: 2108

Alfa AF: 0.0705 Hom.: 704

Bravo AF: 0.0808

Asia WGS AF: 0.0250 AC: 88 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.31
PhyloP100		0.39

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13169538;

hg19: chr5-44570040;