rs16901892

Variant names:

• chr5-44512967-T-C
• rs16901892
• ENST00000671607.2:n.258-8495A>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.258-8495A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0631 in 152,116 control chromosomes in the GnomAD database, including 368 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 0.063 (368 hom., cov: 32)
• Consequence: MRPS30-DT ENST00000671607.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.07 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRPS30-DT	ENST00000671607.2		n.258-8495A>G		intron	N/A
	MRPS30-DT	ENST00000715752.1		n.1089-8495A>G		intron	N/A
	MRPS30-DT	ENST00000715753.1		n.704-2879A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0631 AC: 9589 AN: 151998 Hom.: 367 Cov.: 32

Gnomad AFR AF: 0.0612

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0660

Gnomad ASJ AF: 0.0767

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.0559

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0716

Gnomad OTH AF: 0.0689

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

GnomAD4 genome AF: 0.0631 AC: 9596 AN: 152116 Hom.: 368 Cov.: 32 AF XY: 0.0622 AC XY: 4622 AN XY: 74364

African (AFR) AF: 0.0612 AC: 2542 AN: 41514

American (AMR) AF: 0.0659 AC: 1004 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0767 AC: 266 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5174

South Asian (SAS) AF: 0.0203 AC: 98 AN: 4822

European-Finnish (FIN) AF: 0.0559 AC: 592 AN: 10596

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0717 AC: 4871 AN: 67980

Other (OTH) AF: 0.0677 AC: 143 AN: 2112

Alfa AF: 0.0681 Hom.: 223

Bravo AF: 0.0633

Asia WGS AF: 0.0160 AC: 56 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	2.6
DANN	Benign	0.61
PhyloP100		-0.036

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16901892;

hg19: chr5-44513069;