rs2691678

Variant names:

• chr3-41188832-A-G
• rs2691678
• ENST00000616142.1:n.-209A>G

Variant summary

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

The ENST00000616142.1(MRPS31P1):​n.-209A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,162 control chromosomes in the GnomAD database, including 3,646 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 0.19 (3646 hom., cov: 31)
• Consequence: MRPS31P1 ENST00000616142.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.58

Genes affected

MRPS31P1 (HGNC:29763): (mitochondrial ribosomal protein S31 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRPS31P1	ENST00000616142.1	n.-209A>G		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29154 AN: 152044 Hom.: 3643 Cov.: 31

Gnomad AFR AF: 0.0451

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.0285

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.221

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.192 AC: 29146 AN: 152162 Hom.: 3646 Cov.: 31 AF XY: 0.192 AC XY: 14309 AN XY: 74392

Gnomad4 AFR AF: 0.0450

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.0284

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.218

Alfa AF: 0.234 Hom.: 2071

Bravo AF: 0.175

Asia WGS AF: 0.137 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.2
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2691678; hg19: chr3-41230323;