rs10917686

Variant names:

• chr1-161688700-C-T
• rs10917686
• ENST00000729097.1:n.48-3490G>A

Variant summary

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

The ENST00000729097.1(RPL31P11):​n.48-3490G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,034 control chromosomes in the GnomAD database, including 2,356 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 0.16 (2356 hom., cov: 31)
• Consequence: RPL31P11 ENST00000729097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182
• Publications: 6 publications found

Genes affected

RPL31P11 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.217 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
RPL31P11	ENST00000729097.1	n.48-3490G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23631 AN: 151916 Hom.: 2356 Cov.: 31

Gnomad AFR AF: 0.0458

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.00809

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.155 AC: 23641 AN: 152034 Hom.: 2356 Cov.: 31 AF XY: 0.155 AC XY: 11513 AN XY: 74316

African (AFR) AF: 0.0458 AC: 1901 AN: 41494

American (AMR) AF: 0.177 AC: 2700 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 643 AN: 3466

East Asian (EAS) AF: 0.00811 AC: 42 AN: 5178

South Asian (SAS) AF: 0.212 AC: 1021 AN: 4814

European-Finnish (FIN) AF: 0.175 AC: 1848 AN: 10530

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14962 AN: 67966

Other (OTH) AF: 0.169 AC: 356 AN: 2112

Alfa AF: 0.182 Hom.: 386

Bravo AF: 0.147

Asia WGS AF: 0.120 AC: 416 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.63
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs10917686; hg19: chr1-161658490;