rs10917688

Variant names:

• chr1-161688990-C-T
• rs10917688
• ENST00000729097.1:n.48-3780G>A

Variant summary

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

The ENST00000729097.1(RPL31P11):​n.48-3780G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,140 control chromosomes in the GnomAD database, including 2,361 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 (2361 hom., cov: 31)
• Consequence: RPL31P11 ENST00000729097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182
• Publications: 5 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729097.1. 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
	RPL31P11	ENST00000729097.1		n.48-3780G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23648 AN: 152022 Hom.: 2361 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: 0.00770

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.176

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: 0.156 AC: 23658 AN: 152140 Hom.: 2361 Cov.: 31 AF XY: 0.155 AC XY: 11526 AN XY: 74364

African (AFR) AF: 0.0458 AC: 1904 AN: 41546

American (AMR) AF: 0.177 AC: 2702 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 644 AN: 3470

East Asian (EAS) AF: 0.00772 AC: 40 AN: 5184

South Asian (SAS) AF: 0.213 AC: 1023 AN: 4808

European-Finnish (FIN) AF: 0.176 AC: 1860 AN: 10552

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

European-Non Finnish (NFE) AF: 0.220 AC: 14959 AN: 67970

Other (OTH) AF: 0.169 AC: 358 AN: 2114

Alfa AF: 0.183 Hom.: 521

Bravo AF: 0.147

Asia WGS AF: 0.120 AC: 416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.69
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs10917688; hg19: chr1-161658780;