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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRPS30-DT	ENST00000656315.1	n.2419T>C		non_coding_transcript_exon_variant	Exon 2 of 2
MRPS30-DT	ENST00000671607.2	n.161+65497T>C		intron_variant	Intron 1 of 4
MRPS30-DT	ENST00000715752.1	n.411+2066T>C		intron_variant	Intron 3 of 6

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 v4.3

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

Other links and lift over

dbSNP: rs994793; hg19: chr5-44743247;