rs11746980

Positions:

• chr5-44777776-G-A
• chr5-44777776-G-C
• chr5-44777776-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_109865.1(MRPS30-DT):​n.152+30866C>T variant causes a intron, non coding transcript 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 NR_109865.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.911

Genes affected

MRPS30-DT (HGNC:53420): (MRPS30 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MRPS30-DT	NR_109865.1	n.152+30866C>T		intron_variant, non_coding_transcript_variant
MRPS30-DT	NR_109862.1	n.153-675C>T		intron_variant, non_coding_transcript_variant
MRPS30-DT	NR_109863.1	n.153-675C>T		intron_variant, non_coding_transcript_variant
MRPS30-DT	NR_109864.1	n.152+30866C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MRPS30-DT	ENST00000503452.5	n.136+30866C>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.457

Alfa AF: 0.419 Hom.: 19465

Bravo AF: 0.473

Asia WGS AF: 0.563 AC: 1949 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.6
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11746980; hg19: chr5-44777878;