rs17729322

chr7-23298940-G-T

Variant summary

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

The ENST00000479974.1(MALSU1):n.202G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0508 in 177,800 control chromosomes in the GnomAD database, including 314 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 0.050 (269 hom., cov: 33)
  • Exomes 𝑓: 0.057 (45 hom.)
• Consequence: MALSU1 ENST00000479974.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201

Genes affected

MALSU1 (HGNC:21721): (mitochondrial assembly of ribosomal large subunit 1) Predicted to enable ribosomal large subunit binding activity. Involved in negative regulation of mitochondrial translation and ribosomal large subunit biogenesis. Located in cytosol and mitochondrion. Colocalizes with mitochondrial large ribosomal subunit. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MALSU1	ENST00000479974.1	n.202G>T		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes AF: 0.0499 AC: 7589 AN: 152150 Hom.: 269 Cov.: 33

Gnomad AFR AF: 0.0134

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0353

Gnomad ASJ AF: 0.0401

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0443

Gnomad FIN AF: 0.0536

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0798

Gnomad OTH AF: 0.0402

GnomAD4 exome AF: 0.0566 AC: 1446 AN: 25532 Hom.: 45 Cov.: 0 AF XY: 0.0550 AC XY: 701 AN XY: 12740

Gnomad4 AFR exome AF: 0.0121

Gnomad4 AMR exome AF: 0.0305

Gnomad4 ASJ exome AF: 0.0334

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0536

Gnomad4 FIN exome AF: 0.0600

Gnomad4 NFE exome AF: 0.0673

Gnomad4 OTH exome AF: 0.0555

GnomAD4 genome AF: 0.0499 AC: 7591 AN: 152268 Hom.: 269 Cov.: 33 AF XY: 0.0484 AC XY: 3603 AN XY: 74460

Gnomad4 AFR AF: 0.0133

Gnomad4 AMR AF: 0.0352

Gnomad4 ASJ AF: 0.0401

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0452

Gnomad4 FIN AF: 0.0536

Gnomad4 NFE AF: 0.0799

Gnomad4 OTH AF: 0.0393

Alfa AF: 0.0671 Hom.: 549

Bravo AF: 0.0455

Asia WGS AF: 0.0160 AC: 58 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	1.3
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17729322; hg19: chr7-23338559;