rs8131349

Variant names:

• chr21-34199605-G-A
• rs8131349
• ENST00000362077.4:n.295-15895G>A

Your query was ambiguous. Multiple possible variants found:

• chr21-34199605-G-A
• chr21-34199605-G-C
• chr21-34199605-G-T

Variant summary

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

The ENST00000362077.4(ENSG00000272657):​n.295-15895G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0525 in 151,244 control chromosomes in the GnomAD database, including 332 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 0.052 (332 hom., cov: 30)
• Consequence: ENSG00000272657 ENST00000362077.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672

Genes affected

ENSG00000272657 (HGNC:14051): (mitochondrial ribosomal protein S6) Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 28S subunit protein that belongs to the ribosomal protein S6P family. Pseudogenes corresponding to this gene are found on chromosomes 1p and 12q. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.178 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
ENSG00000272657	ENST00000362077.4	n.295-15895G>A		intron_variant	Intron 2 of 5	3		ENSP00000520522.1

Frequencies

GnomAD3 genomes AF: 0.0524 AC: 7926 AN: 151132 Hom.: 329 Cov.: 30

Gnomad AFR AF: 0.0160

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0383

Gnomad ASJ AF: 0.0912

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0893

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0525

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0525 AC: 7939 AN: 151244 Hom.: 332 Cov.: 30 AF XY: 0.0550 AC XY: 4063 AN XY: 73812

Gnomad4 AFR AF: 0.0160

Gnomad4 AMR AF: 0.0383

Gnomad4 ASJ AF: 0.0912

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.0893

Gnomad4 NFE AF: 0.0525

Gnomad4 OTH AF: 0.0578

Alfa AF: 0.0504 Hom.: 196

Bravo AF: 0.0465

Asia WGS AF: 0.185 AC: 643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.93
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8131349; hg19: chr21-35571906;