7-23298940-G-T

Variant names:

• chr7-23298940-G-T
• rs17729322
• ENST00000479974.1:n.202G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000479974.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MALSU1	ENST00000479974.1	TSL:2	n.202G>T		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.0121 AC: 13 AN: 1074

American (AMR) AF: 0.0305 AC: 24 AN: 788

Ashkenazi Jewish (ASJ) AF: 0.0334 AC: 37 AN: 1108

East Asian (EAS) AF: 0.00 AC: 0 AN: 1512

South Asian (SAS) AF: 0.0536 AC: 27 AN: 504

European-Finnish (FIN) AF: 0.0600 AC: 76 AN: 1266

Middle Eastern (MID) AF: 0.0238 AC: 4 AN: 168

European-Non Finnish (NFE) AF: 0.0673 AC: 1167 AN: 17346

Other (OTH) AF: 0.0555 AC: 98 AN: 1766

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

African (AFR) AF: 0.0133 AC: 554 AN: 41572

American (AMR) AF: 0.0352 AC: 538 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0401 AC: 139 AN: 3470

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5180

South Asian (SAS) AF: 0.0452 AC: 218 AN: 4822

European-Finnish (FIN) AF: 0.0536 AC: 568 AN: 10604

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0799 AC: 5430 AN: 68000

Other (OTH) AF: 0.0393 AC: 83 AN: 2110

Alfa AF: 0.0653 Hom.: 925

Bravo AF: 0.0455

Asia WGS AF: 0.0160 AC: 58 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.77
PhyloP100		-0.20
PromoterAI		-0.018	Neutral

Splicing

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

Other links and lift over

dbSNP: rs17729322; hg19: chr7-23338559;