3-41189163-T-C

Position:

• chr3-41189163-T-C

Variant summary

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

The ENST00000616142.1(MRPS31P1):​n.123T>C 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 0.418 in 165,590 control chromosomes in the GnomAD database, including 15,971 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 0.42 (14845 hom., cov: 31)
  • Exomes 𝑓: 0.39 (1126 hom.)
• Consequence: MRPS31P1 ENST00000616142.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255

Genes affected

MRPS31P1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MRPS31P1		n.41189163T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MRPS31P1	ENST00000616142.1	n.123T>C		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63883 AN: 151760 Hom.: 14843 Cov.: 31

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.457

GnomAD4 exome AF: 0.389 AC: 5333 AN: 13710 Hom.: 1126 Cov.: 0 AF XY: 0.383 AC XY: 2684 AN XY: 7008

Gnomad4 AFR exome AF: 0.214

Gnomad4 AMR exome AF: 0.141

Gnomad4 ASJ exome AF: 0.269

Gnomad4 EAS exome AF: 0.414

Gnomad4 SAS exome AF: 0.326

Gnomad4 FIN exome AF: 0.409

Gnomad4 NFE exome AF: 0.256

Gnomad4 OTH exome AF: 0.360

GnomAD4 genome AF: 0.421 AC: 63895 AN: 151880 Hom.: 14845 Cov.: 31 AF XY: 0.422 AC XY: 31335 AN XY: 74206

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.459

Alfa AF: 0.492 Hom.: 32733

Bravo AF: 0.403

Asia WGS AF: 0.544 AC: 1885 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.82
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7630377; hg19: chr3-41230654;