10-52389483-A-C

Variant names:

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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL31P44		n.52389483A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL31P44	ENST00000447680.1	n.6T>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

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 v4.3

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

Other links and lift over

dbSNP: rs6480837; hg19: chr10-54149243;