3-41189163-T-C

Variant names:

• chr3-41189163-T-C
• rs7630377
• ENST00000616142.1:n.123T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

Genes affected

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

ENSG00000233919 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000616142.1. 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
	MRPS31P1	ENST00000616142.1	TSL:6	n.123T>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000233919	ENST00000775824.1		n.56+7321A>G		intron	N/A

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

African (AFR) AF: 0.214 AC: 21 AN: 98

American (AMR) AF: 0.141 AC: 31 AN: 220

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 42 AN: 156

East Asian (EAS) AF: 0.414 AC: 24 AN: 58

South Asian (SAS) AF: 0.326 AC: 174 AN: 534

European-Finnish (FIN) AF: 0.409 AC: 3960 AN: 9690

Middle Eastern (MID) AF: 0.530 AC: 561 AN: 1058

European-Non Finnish (NFE) AF: 0.256 AC: 399 AN: 1560

Other (OTH) AF: 0.360 AC: 121 AN: 336

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

African (AFR) AF: 0.229 AC: 9491 AN: 41442

American (AMR) AF: 0.396 AC: 6035 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1934 AN: 3468

East Asian (EAS) AF: 0.693 AC: 3581 AN: 5170

South Asian (SAS) AF: 0.539 AC: 2586 AN: 4802

European-Finnish (FIN) AF: 0.441 AC: 4640 AN: 10524

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34104 AN: 67926

Other (OTH) AF: 0.459 AC: 964 AN: 2102

Alfa AF: 0.476 Hom.: 68725

Bravo AF: 0.403

Asia WGS AF: 0.544 AC: 1885 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.82
DANN	Benign	0.61
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs7630377; hg19: chr3-41230654;