rs994793

Positions:

• chr5-44743145-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

MRPS30-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.44743145A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MRPS30-DT	ENST00000656315.1	n.2419T>C		non_coding_transcript_exon_variant	2/2

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

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.463

Alfa AF: 0.430 Hom.: 8258

Bravo AF: 0.487

Asia WGS AF: 0.562 AC: 1946 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs994793; hg19: chr5-44743247;