5-44702405-T-C

Variant names:

• chr5-44702405-T-C
• rs920329
• ENST00000671607.2:n.162-43848A>G

Variant summary

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

The ENST00000671607.2(MRPS30-DT):​n.162-43848A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 151,532 control chromosomes in the GnomAD database, including 18,374 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 0.48 (18374 hom., cov: 32)
• Consequence: MRPS30-DT ENST00000671607.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 10 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 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	ENST00000671607.2	n.162-43848A>G		intron_variant	Intron 1 of 4
MRPS30-DT	ENST00000715752.1	n.411+42806A>G		intron_variant	Intron 3 of 6
MRPS30-DT	ENST00000715753.1	n.607+30488A>G		intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes AF: 0.481 AC: 72806 AN: 151414 Hom.: 18322 Cov.: 32

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.481 AC: 72910 AN: 151532 Hom.: 18374 Cov.: 32 AF XY: 0.485 AC XY: 35924 AN XY: 74058

African (AFR) AF: 0.623 AC: 25825 AN: 41426

American (AMR) AF: 0.497 AC: 7535 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1503 AN: 3458

East Asian (EAS) AF: 0.561 AC: 2884 AN: 5142

South Asian (SAS) AF: 0.507 AC: 2444 AN: 4820

European-Finnish (FIN) AF: 0.401 AC: 4224 AN: 10538

Middle Eastern (MID) AF: 0.459 AC: 134 AN: 292

European-Non Finnish (NFE) AF: 0.400 AC: 27084 AN: 67668

Other (OTH) AF: 0.464 AC: 976 AN: 2102

Alfa AF: 0.293 Hom.: 708

Bravo AF: 0.496

Asia WGS AF: 0.574 AC: 1993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.72
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs920329; hg19: chr5-44702507; COSMIC: COSV73949921;