10-57982982-C-T

Variant names:

• chr10-57982982-C-T
• rs7898163
• ENST00000603189.1:n.698C>T

Variant summary

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

The ENST00000603189.1(MRPS35P3):​n.698C>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 0.0783 in 152,138 control chromosomes in the GnomAD database, including 1,260 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 0.078 (1260 hom., cov: 34)
  • Failed GnomAD Quality Control
• Consequence: MRPS35P3 ENST00000603189.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.968

Genes affected

MRPS35P3 (HGNC:29770): (mitochondrial ribosomal protein S35 pseudogene 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRPS35P3		n.57982982C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRPS35P3	ENST00000603189.1	n.698C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.0782 AC: 11881 AN: 152020 Hom.: 1255 Cov.: 34

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0379

Gnomad ASJ AF: 0.0433

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00830

Gnomad FIN AF: 0.00349

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0129

Gnomad OTH AF: 0.0688

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0783 AC: 11920 AN: 152138 Hom.: 1260 Cov.: 34 AF XY: 0.0760 AC XY: 5650 AN XY: 74376

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.0377

Gnomad4 ASJ AF: 0.0433

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00789

Gnomad4 FIN AF: 0.00349

Gnomad4 NFE AF: 0.0130

Gnomad4 OTH AF: 0.0681

Alfa AF: 0.00696 Hom.: 2

Bravo AF: 0.0889

Asia WGS AF: 0.0240 AC: 84 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.6
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: rs7898163; hg19: chr10-59742742;