Variant chr16-11281009-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_002761.3(PRM1):c.139C>A(p.Arg47=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 1,613,064 control chromosomes in the GnomAD database, including 378,359 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.62 ( 29914 hom., cov: 31)

Exomes 𝑓: 0.68 ( 348445 hom. )

Consequence

PRM1
NM_002761.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.628

Variant links:

Genes affected

PRM1 (HGNC:9447): (protamine 1) Predicted to enable DNA binding activity. Predicted to be involved in DNA packaging. Predicted to act upstream of or within nucleus organization and spermatid development. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

PRM1 links:

RMI2 (HGNC:28349): (RecQ mediated genome instability 2) RMI2 is a component of the BLM (RECQL3; MIM 604610) complex, which plays a role in homologous recombination-dependent DNA repair and is essential for genome stability (Xu et al., 2008 [PubMed 18923082]).[supplied by OMIM, Nov 2008]

RMI2 links:

LOC105371082 (HGNC:):

LOC105371082 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 16-11281009-G-T is Benign according to our data. Variant chr16-11281009-G-T is described in ClinVar as [Benign]. Clinvar id is 1272307.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.628 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRM1	NM_002761.3 linkuse as main transcript	c.139C>A	p.Arg47=	synonymous_variant	2/2	ENST00000312511.4
LOC105371082	XR_933070.4 linkuse as main transcript	n.178+31231G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRM1	ENST00000312511.4 linkuse as main transcript	c.139C>A	p.Arg47=	synonymous_variant	2/2	1	NM_002761.3	P1
RMI2	ENST00000572173.1 linkuse as main transcript	c.-515-14207G>T		intron_variant		1			Q96E14-2
RMI2	ENST00000573910.1 linkuse as main transcript	n.160+31231G>T		intron_variant, non_coding_transcript_variant		3
RMI2	ENST00000649869.1 linkuse as main transcript	n.152+31231G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.617

AC:

93671

AN:

151888

Hom.:

29908

Cov.:

show subpopulations

Gnomad AFR

AF:

0.541

Gnomad AMI

AF:

0.767

Gnomad AMR

AF:

0.493

Gnomad ASJ

AF:

0.550

Gnomad EAS

AF:

0.319

Gnomad SAS

AF:

0.493

Gnomad FIN

AF:

0.692

Gnomad MID

AF:

0.547

Gnomad NFE

AF:

0.712

Gnomad OTH

AF:

0.616

GnomAD3 exomes

AF:

0.584

AC:

146850

AN:

251478

Hom.:

46041

AF XY:

0.592

AC XY:

80436

AN XY:

135916

show subpopulations

Gnomad AFR exome

AF:

0.529

Gnomad AMR exome

AF:

0.352

Gnomad ASJ exome

AF:

0.542

Gnomad EAS exome

AF:

0.311

Gnomad SAS exome

AF:

0.507

Gnomad FIN exome

AF:

0.690

Gnomad NFE exome

AF:

0.709

Gnomad OTH exome

AF:

0.617

GnomAD4 exome

AF:

0.680

AC:

994247

AN:

1461058

Hom.:

348445

Cov.:

AF XY:

0.676

AC XY:

491431

AN XY:

726888

show subpopulations

Gnomad4 AFR exome

AF:

0.531

Gnomad4 AMR exome

AF:

0.366

Gnomad4 ASJ exome

AF:

0.544

Gnomad4 EAS exome

AF:

0.293

Gnomad4 SAS exome

AF:

0.506

Gnomad4 FIN exome

AF:

0.697

Gnomad4 NFE exome

AF:

0.730

Gnomad4 OTH exome

AF:

0.656

GnomAD4 genome

AF:

0.616

AC:

93682

AN:

152006

Hom.:

29914

Cov.:

AF XY:

0.607

AC XY:

45099

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.541

Gnomad4 AMR

AF:

0.492

Gnomad4 ASJ

AF:

0.550

Gnomad4 EAS

AF:

0.319

Gnomad4 SAS

AF:

0.493

Gnomad4 FIN

AF:

0.692

Gnomad4 NFE

AF:

0.712

Gnomad4 OTH

AF:

0.611

Alfa

AF:

0.676

Hom.:

44033

Bravo

AF:

0.595

Asia WGS

AF:

0.423

AC:

1473

AN:

3478

EpiCase

AF:

0.695

EpiControl

AF:

0.683

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	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.1

DANN

Benign

0.52

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