1-161690906-G-T

Variant names:

• chr1-161690906-G-T
• rs6697139
• ENST00000729097.1:n.48-5696C>A

Variant summary

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

The ENST00000729097.1(RPL31P11):​n.48-5696C>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 151,806 control chromosomes in the GnomAD database, including 2,368 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 (2368 hom., cov: 32)
• Consequence: RPL31P11 ENST00000729097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 13 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.218 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPL31P11	ENST00000729097.1		n.48-5696C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23666 AN: 151688 Hom.: 2368 Cov.: 32

Gnomad AFR AF: 0.0459

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.00809

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.221

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: 23676 AN: 151806 Hom.: 2368 Cov.: 32 AF XY: 0.156 AC XY: 11546 AN XY: 74200

African (AFR) AF: 0.0460 AC: 1901 AN: 41370

American (AMR) AF: 0.177 AC: 2699 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 640 AN: 3466

East Asian (EAS) AF: 0.00810 AC: 42 AN: 5182

South Asian (SAS) AF: 0.214 AC: 1030 AN: 4808

European-Finnish (FIN) AF: 0.177 AC: 1859 AN: 10478

Middle Eastern (MID) AF: 0.272 AC: 79 AN: 290

European-Non Finnish (NFE) AF: 0.220 AC: 14980 AN: 67944

Other (OTH) AF: 0.170 AC: 358 AN: 2112

Alfa AF: 0.201 Hom.: 4994

Bravo AF: 0.147

Asia WGS AF: 0.120 AC: 416 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.4
DANN	Benign	0.64
PhyloP100		0.0020

Splicing

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

Other links and lift over

dbSNP: rs6697139; hg19: chr1-161660696;