Variant chr10-102152452-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_004741.5(NOLC1):c.42G>A(p.Leu14Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00653 in 1,613,210 control chromosomes in the GnomAD database, including 54 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0055 ( 4 hom., cov: 33)

Exomes 𝑓: 0.0066 ( 50 hom. )

Consequence

NOLC1
NM_004741.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0450

Variant links:

Genes affected

NOLC1 (HGNC:15608): (nucleolar and coiled-body phosphoprotein 1) Enables protein heterodimerization activity and protein-macromolecule adaptor activity. Involved in neural crest cell development; neural crest formation; and regulation of translation. Located in fibrillar center. [provided by Alliance of Genome Resources, Apr 2022]

NOLC1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 10-102152452-G-A is Benign according to our data. Variant chr10-102152452-G-A is described in ClinVar as [Benign]. Clinvar id is 784653.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.045 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOLC1	NM_004741.5 link	c.42G>A	p.Leu14Leu	synonymous_variant	Exon 1 of 13	ENST00000605788.6	NP_004732.2	Q14978-1Q96J17B2RAU8
NOLC1	NM_001284388.2 link	c.42G>A	p.Leu14Leu	synonymous_variant	Exon 1 of 13		NP_001271317.1	Q14978-2B2RAU8
NOLC1	NM_001284389.2 link	c.42G>A	p.Leu14Leu	synonymous_variant	Exon 1 of 13		NP_001271318.1	Q14978-3
NOLC1	XM_005270273.3 link	c.42G>A	p.Leu14Leu	synonymous_variant	Exon 1 of 13		XP_005270330.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOLC1	ENST00000605788.6 link	c.42G>A	p.Leu14Leu	synonymous_variant	Exon 1 of 13	1	NM_004741.5	ENSP00000474710.2		Q14978-1

Frequencies

GnomAD3 genomes

AF:

0.00548

AC:

834

AN:

152252

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00128

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00216

Gnomad ASJ

AF:

0.00519

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.0111

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00866

Gnomad OTH

AF:

0.00621

GnomAD3 exomes

AF:

0.00590

AC:

1464

AN:

248282

Hom.:

AF XY:

0.00623

AC XY:

838

AN XY:

134498

show subpopulations

Gnomad AFR exome

AF:

0.000985

Gnomad AMR exome

AF:

0.00191

Gnomad ASJ exome

AF:

0.00834

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00359

Gnomad FIN exome

AF:

0.0129

Gnomad NFE exome

AF:

0.00791

Gnomad OTH exome

AF:

0.00622

GnomAD4 exome

AF:

0.00664

AC:

9705

AN:

1460840

Hom.:

Cov.:

AF XY:

0.00660

AC XY:

4796

AN XY:

726768

show subpopulations

Gnomad4 AFR exome

AF:

0.000866

Gnomad4 AMR exome

AF:

0.00195

Gnomad4 ASJ exome

AF:

0.00715

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00384

Gnomad4 FIN exome

AF:

0.0132

Gnomad4 NFE exome

AF:

0.00722

Gnomad4 OTH exome

AF:

0.00575

GnomAD4 genome

AF:

0.00547

AC:

834

AN:

152370

Hom.:

Cov.:

AF XY:

0.00552

AC XY:

411

AN XY:

74510

show subpopulations

Gnomad4 AFR

AF:

0.00127

Gnomad4 AMR

AF:

0.00216

Gnomad4 ASJ

AF:

0.00519

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00207

Gnomad4 FIN

AF:

0.0111

Gnomad4 NFE

AF:

0.00866

Gnomad4 OTH

AF:

0.00614

Alfa

AF:

0.00721

Hom.:

Bravo

AF:

0.00462

EpiCase

AF:

0.00823

EpiControl

AF:

0.00622

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

DANN

Benign

0.90

RBP_binding_hub_radar

1.1

RBP_regulation_power_radar

2.8

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over