rs6480837

Variant names:

• chr10-52389483-A-C
• rs6480837
• ENST00000447680.1:n.6T>G

Your query was ambiguous. Multiple possible variants found:

• chr10-52389483-A-C
• chr10-52389483-A-G
• chr10-52389483-A-T

Variant summary

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

The ENST00000447680.1(RPL31P44):​n.6T>G 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 0.676 in 475,018 control chromosomes in the GnomAD database, including 111,494 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 0.72 (40340 hom., cov: 30)
  • Exomes 𝑓: 0.66 (71154 hom.)
• Consequence: RPL31P44 ENST00000447680.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 1 publications found

Genes affected

RPL31P44 (HGNC:35523): (ribosomal protein L31 pseudogene 44)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447680.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPL31P44	ENST00000447680.1	TSL:6	n.6T>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108538 AN: 151760 Hom.: 40268 Cov.: 30

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.663

GnomAD4 exome AF: 0.657 AC: 212459 AN: 323140 Hom.: 71154 Cov.: 0 AF XY: 0.654 AC XY: 118931 AN XY: 181788

African (AFR) AF: 0.913 AC: 8052 AN: 8820

American (AMR) AF: 0.625 AC: 15018 AN: 24036

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 4203 AN: 7504

East Asian (EAS) AF: 0.928 AC: 14299 AN: 15414

South Asian (SAS) AF: 0.644 AC: 31756 AN: 49334

European-Finnish (FIN) AF: 0.618 AC: 16768 AN: 27112

Middle Eastern (MID) AF: 0.563 AC: 546 AN: 970

European-Non Finnish (NFE) AF: 0.639 AC: 111652 AN: 174696

Other (OTH) AF: 0.666 AC: 10165 AN: 15254

GnomAD4 genome AF: 0.715 AC: 108668 AN: 151878 Hom.: 40340 Cov.: 30 AF XY: 0.713 AC XY: 52881 AN XY: 74186

African (AFR) AF: 0.912 AC: 37835 AN: 41470

American (AMR) AF: 0.635 AC: 9691 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1861 AN: 3464

East Asian (EAS) AF: 0.932 AC: 4781 AN: 5132

South Asian (SAS) AF: 0.665 AC: 3203 AN: 4814

European-Finnish (FIN) AF: 0.609 AC: 6395 AN: 10500

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.629 AC: 42739 AN: 67934

Other (OTH) AF: 0.667 AC: 1410 AN: 2114

Alfa AF: 0.594 Hom.: 1924

Bravo AF: 0.725

Asia WGS AF: 0.838 AC: 2910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	2.0
DANN	Benign	0.52
PhyloP100		1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6480837;

hg19: chr10-54149243;