rs7277241

Variant names:

• chr21-34172341-G-A
• rs7277241
• ENST00000362077.5:n.186-43159G>A

Your query was ambiguous. Multiple possible variants found:

• chr21-34172341-G-A
• chr21-34172341-G-C
• chr21-34172341-G-T

Variant summary

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

The ENST00000362077.5(MRPS6):​n.186-43159G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,188 control chromosomes in the GnomAD database, including 2,281 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 0.13 (2281 hom., cov: 32)
• Consequence: MRPS6 ENST00000362077.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 1 publications found

Genes affected

MRPS6 (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]

LINC00310 (HGNC:16414): (long intergenic non-protein coding RNA 310)

ENSG00000304893 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.295 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
MRPS6	ENST00000362077.5	n.186-43159G>A		intron_variant	Intron 2 of 6	3		ENSP00000520522.1
LINC00310	ENST00000630751.2	n.129+14489G>A		intron_variant	Intron 1 of 2	5
MRPS6	ENST00000715810.1	n.186-8370G>A		intron_variant	Intron 2 of 3			ENSP00000520521.1
ENSG00000304893	ENST00000806986.1	n.84+2663C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20395 AN: 152070 Hom.: 2279 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.0613

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0537

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.134 AC: 20434 AN: 152188 Hom.: 2281 Cov.: 32 AF XY: 0.134 AC XY: 9945 AN XY: 74414

African (AFR) AF: 0.299 AC: 12408 AN: 41504

American (AMR) AF: 0.0695 AC: 1063 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0613 AC: 213 AN: 3472

East Asian (EAS) AF: 0.203 AC: 1049 AN: 5170

South Asian (SAS) AF: 0.129 AC: 621 AN: 4820

European-Finnish (FIN) AF: 0.103 AC: 1093 AN: 10608

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0537 AC: 3653 AN: 68002

Other (OTH) AF: 0.123 AC: 260 AN: 2108

Alfa AF: 0.0782 Hom.: 584

Bravo AF: 0.138

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.52
PhyloP100		0.069

Splicing

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

Other links and lift over

dbSNP: rs7277241; hg19: chr21-35544641;