chr5-44694433-G-A

Variant names:

• chr5-44694433-G-A
• rs12515012
• ENST00000671607.2:n.162-35876C>T

Variant summary

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

The ENST00000671607.2(MRPS30-DT):​n.162-35876C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,022 control chromosomes in the GnomAD database, including 12,479 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 0.40 (12479 hom., cov: 32)
• Consequence: MRPS30-DT ENST00000671607.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 7 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671607.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRPS30-DT	ENST00000671607.2		n.162-35876C>T		intron	N/A
	MRPS30-DT	ENST00000715752.1		n.412-35295C>T		intron	N/A
	MRPS30-DT	ENST00000715753.1		n.608-35876C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60890 AN: 151904 Hom.: 12454 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.401 AC: 60937 AN: 152022 Hom.: 12479 Cov.: 32 AF XY: 0.406 AC XY: 30169 AN XY: 74306

African (AFR) AF: 0.363 AC: 15027 AN: 41448

American (AMR) AF: 0.449 AC: 6854 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1481 AN: 3472

East Asian (EAS) AF: 0.504 AC: 2593 AN: 5148

South Asian (SAS) AF: 0.499 AC: 2408 AN: 4824

European-Finnish (FIN) AF: 0.395 AC: 4179 AN: 10578

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.399 AC: 27092 AN: 67964

Other (OTH) AF: 0.414 AC: 873 AN: 2110

Alfa AF: 0.406 Hom.: 1572

Bravo AF: 0.402

Asia WGS AF: 0.510 AC: 1773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.17
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs12515012; hg19: chr5-44694535;