rs2691678

Variant names:

• chr3-41188832-A-G
• rs2691678
• ENST00000775824.1:n.56+7652T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000775824.1(ENSG00000233919):​n.56+7652T>C variant causes a intron 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: ENSG00000233919 ENST00000775824.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.58
• Publications: 4 publications found

Genes affected

ENSG00000233919 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000233919	ENST00000775824.1	n.56+7652T>C		intron_variant	Intron 1 of 2
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

African (AFR) AF: 0.0450 AC: 1869 AN: 41540

American (AMR) AF: 0.192 AC: 2935 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1147 AN: 3472

East Asian (EAS) AF: 0.0284 AC: 147 AN: 5182

South Asian (SAS) AF: 0.242 AC: 1164 AN: 4812

European-Finnish (FIN) AF: 0.257 AC: 2719 AN: 10586

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18348 AN: 67984

Other (OTH) AF: 0.218 AC: 461 AN: 2112

Alfa AF: 0.228 Hom.: 8617

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
PhyloP100		2.6

Splicing

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

Other links and lift over

dbSNP: rs2691678; hg19: chr3-41230323;