rs994793

Variant names:

• chr5-44743145-A-G
• rs994793
• ENST00000656315.1:n.2419T>C

Variant summary

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

The ENST00000656315.1(MRPS30-DT):​n.2419T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,828 control chromosomes in the GnomAD database, including 17,789 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 0.47 (17789 hom., cov: 32)
• Consequence: MRPS30-DT ENST00000656315.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 5 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656315.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRPS30-DT	ENST00000656315.1		n.2419T>C		non_coding_transcript_exon	Exon 2 of 2
	MRPS30-DT	ENST00000671607.2		n.161+65497T>C		intron	N/A
	MRPS30-DT	ENST00000715752.1		n.411+2066T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.475 AC: 71992 AN: 151710 Hom.: 17742 Cov.: 32

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.475 AC: 72097 AN: 151828 Hom.: 17789 Cov.: 32 AF XY: 0.477 AC XY: 35359 AN XY: 74176

African (AFR) AF: 0.597 AC: 24720 AN: 41440

American (AMR) AF: 0.478 AC: 7276 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1497 AN: 3466

East Asian (EAS) AF: 0.552 AC: 2830 AN: 5130

South Asian (SAS) AF: 0.486 AC: 2343 AN: 4824

European-Finnish (FIN) AF: 0.398 AC: 4201 AN: 10550

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.410 AC: 27825 AN: 67884

Other (OTH) AF: 0.463 AC: 976 AN: 2106

Alfa AF: 0.427 Hom.: 11655

Bravo AF: 0.487

Asia WGS AF: 0.562 AC: 1946 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.1
DANN	Benign	0.78
PhyloP100		-0.23

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: rs994793;

hg19: chr5-44743247;