rs2062140

Variant names:

• chr5-44496313-G-A
• rs2062140
• ENST00000505706.1:n.409-520C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000505706.1(MRPS30-DT):​n.409-520C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0663 in 152,134 control chromosomes in the GnomAD database, including 409 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 0.066 (409 hom., cov: 32)
• Consequence: MRPS30-DT ENST00000505706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.674
• Publications: 2 publications found

Genes affected

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

LINC02224 (HGNC:53093): (long intergenic non-protein coding RNA 2224)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0714 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505706.1. 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
	LINC02224	NR_131946.1		n.451-520C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRPS30-DT	ENST00000505706.1	TSL:4	n.409-520C>T		intron	N/A
	MRPS30-DT	ENST00000671607.2		n.549-520C>T		intron	N/A
	MRPS30-DT	ENST00000715752.1		n.1380-520C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0663 AC: 10081 AN: 152016 Hom.: 408 Cov.: 32

Gnomad AFR AF: 0.0736

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0660

Gnomad ASJ AF: 0.0749

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0205

Gnomad FIN AF: 0.0558

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.0714

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0663 AC: 10087 AN: 152134 Hom.: 409 Cov.: 32 AF XY: 0.0650 AC XY: 4837 AN XY: 74394

African (AFR) AF: 0.0736 AC: 3054 AN: 41508

American (AMR) AF: 0.0659 AC: 1006 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0749 AC: 260 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5178

South Asian (SAS) AF: 0.0205 AC: 99 AN: 4822

European-Finnish (FIN) AF: 0.0558 AC: 591 AN: 10592

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.0714 AC: 4854 AN: 67976

Other (OTH) AF: 0.0676 AC: 143 AN: 2116

Alfa AF: 0.0705 Hom.: 660

Bravo AF: 0.0673

Asia WGS AF: 0.0160 AC: 56 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	16
DANN	Benign	0.86
PhyloP100		0.67

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: rs2062140;

hg19: chr5-44496415;