2-101002870-G-A

Variant names:

• chr2-101002870-G-A
• rs17025161
• NM_000993.5:c.107+62G>A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000993.5(RPL31):​c.107+62G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00671 in 1,211,786 control chromosomes in the GnomAD database, including 388 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.030 (246 hom., cov: 32)
  • Exomes 𝑓: 0.0034 (142 hom.)
• Consequence: RPL31 NM_000993.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 1.12

Genes affected

RPL31 (HGNC:10334): (ribosomal protein L31) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L31E family of ribosomal proteins. It is located in the cytoplasm. Higher levels of expression of this gene in familial adenomatous polyps compared to matched normal tissues have been observed. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 2-101002870-G-A is Benign according to our data. Variant chr2-101002870-G-A is described in ClinVar as [Benign]. Clinvar id is 1251780.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL31	NM_000993.5	c.107+62G>A		intron_variant	Intron 2 of 4	ENST00000264258.8	NP_000984.1
RPL31	NM_001098577.3	c.107+62G>A		intron_variant	Intron 2 of 4		NP_001092047.1
RPL31	NM_001099693.2	c.107+62G>A		intron_variant	Intron 2 of 3		NP_001093163.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL31	ENST00000264258.8	c.107+62G>A		intron_variant	Intron 2 of 4	1	NM_000993.5	ENSP00000264258.3

Frequencies

GnomAD3 genomes AF: 0.0297 AC: 4508 AN: 152028 Hom.: 245 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0125

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000323

Gnomad OTH AF: 0.0191

GnomAD4 exome AF: 0.00342 AC: 3620 AN: 1059640 Hom.: 142 AF XY: 0.00292 AC XY: 1583 AN XY: 542946

Gnomad4 AFR exome AF: 0.102 AC: 2620 AN: 25592

Gnomad4 AMR exome AF: 0.00668 AC: 282 AN: 42196

Gnomad4 ASJ exome AF: 0.00143 AC: 33 AN: 23014

Gnomad4 EAS exome AF: 0.00 AC: 0 AN: 37666

Gnomad4 SAS exome AF: 0.000116 AC: 9 AN: 77750

Gnomad4 FIN exome AF: 0.00 AC: 0 AN: 52824

Gnomad4 NFE exome AF: 0.000413 AC: 309 AN: 748694

Gnomad4 Remaining exome AF: 0.00708 AC: 332 AN: 46924

GnomAD4 genome AF: 0.0297 AC: 4515 AN: 152146 Hom.: 246 Cov.: 32 AF XY: 0.0289 AC XY: 2152 AN XY: 74374

Gnomad4 AFR AF: 0.103 AC: 0.102667 AN: 0.102667

Gnomad4 AMR AF: 0.0125 AC: 0.0124869 AN: 0.0124869

Gnomad4 ASJ AF: 0.000865 AC: 0.000864553 AN: 0.000864553

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.000208 AC: 0.000207555 AN: 0.000207555

Gnomad4 FIN AF: 0.00 AC: 0 AN: 0

Gnomad4 NFE AF: 0.000323 AC: 0.000323472 AN: 0.000323472

Gnomad4 OTH AF: 0.0189 AC: 0.0189394 AN: 0.0189394

Alfa AF: 0.0110 Hom.: 85

Bravo AF: 0.0341

Asia WGS AF: 0.00520 AC: 19 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

May 24, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.3
DANN	Benign	0.64
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs17025161; hg19: chr2-101619332;