5-44709039-A-G

Variant names:

• chr5-44709039-A-G
• rs16901937
• ENST00000671607.2:n.162-50482T>C

Variant summary

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

The ENST00000671607.2(MRPS30-DT):​n.162-50482T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 152,016 control chromosomes in the GnomAD database, including 12,066 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 0.39 (12066 hom., cov: 32)
• Consequence: MRPS30-DT ENST00000671607.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13
• Publications: 8 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 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.162-50482T>C		intron	N/A
	MRPS30-DT	ENST00000715752.1		n.411+36172T>C		intron	N/A
	MRPS30-DT	ENST00000715753.1		n.607+23854T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59535 AN: 151896 Hom.: 12042 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.392 AC: 59581 AN: 152016 Hom.: 12066 Cov.: 32 AF XY: 0.398 AC XY: 29529 AN XY: 74280

African (AFR) AF: 0.321 AC: 13329 AN: 41502

American (AMR) AF: 0.452 AC: 6885 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1496 AN: 3472

East Asian (EAS) AF: 0.505 AC: 2597 AN: 5144

South Asian (SAS) AF: 0.501 AC: 2416 AN: 4826

European-Finnish (FIN) AF: 0.397 AC: 4198 AN: 10566

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.403 AC: 27365 AN: 67950

Other (OTH) AF: 0.410 AC: 865 AN: 2110

Alfa AF: 0.403 Hom.: 6104

Bravo AF: 0.392

Asia WGS AF: 0.508 AC: 1766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.2
DANN	Benign	0.71
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs16901937; hg19: chr5-44709141;