5-44777776-G-A

Variant names:

• chr5-44777776-G-A
• rs11746980
• ENST00000503179.6:n.245+133C>T

Variant summary

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

The ENST00000503452.6(MRPS30-DT):​n.136+30866C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,012 control chromosomes in the GnomAD database, including 16,823 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 0.46 (16823 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: MRPS30-DT ENST00000503452.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.911
• Publications: 6 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 = 0.55 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503452.6. 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
	MRPS30-DT	NR_109862.1		n.153-675C>T		intron	N/A
	MRPS30-DT	NR_109863.1		n.153-675C>T		intron	N/A
	MRPS30-DT	NR_109864.1		n.152+30866C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRPS30-DT	ENST00000503179.6	TSL:4	n.245+133C>T		intron	N/A
	MRPS30-DT	ENST00000503452.6	TSL:2	n.136+30866C>T		intron	N/A
	MRPS30-DT	ENST00000505302.2	TSL:2	n.148+30866C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70330 AN: 151892 Hom.: 16781 Cov.: 33

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.463 AC: 70423 AN: 152012 Hom.: 16823 Cov.: 33 AF XY: 0.466 AC XY: 34610 AN XY: 74296

African (AFR) AF: 0.556 AC: 23048 AN: 41480

American (AMR) AF: 0.474 AC: 7244 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1497 AN: 3466

East Asian (EAS) AF: 0.552 AC: 2851 AN: 5166

South Asian (SAS) AF: 0.487 AC: 2347 AN: 4824

European-Finnish (FIN) AF: 0.400 AC: 4223 AN: 10564

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27820 AN: 67928

Other (OTH) AF: 0.457 AC: 965 AN: 2112

Alfa AF: 0.425 Hom.: 27737

Bravo AF: 0.473

Asia WGS AF: 0.563 AC: 1949 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.6
DANN	Benign	0.57
PhyloP100		0.91
Mutation Taster		=70/30	polymorphism

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: rs11746980;

hg19: chr5-44777878;