Variant rs627897 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_015602.4(TOR1AIP1):c.1503G>A(p.Ala501=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.95 in 1,614,166 control chromosomes in the GnomAD database, including 728,840 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.93 ( 66292 hom., cov: 33)

Exomes 𝑓: 0.95 ( 662548 hom. )

Consequence

TOR1AIP1
NM_015602.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.0140

Variant links:

Genes affected

TOR1AIP1 (HGNC:29456): (torsin 1A interacting protein 1) This gene encodes a type 2 integral membrane protein that binds A- and B-type lamins. The encoded protein localizes to the inner nuclear membrane and may be involved in maintaining the attachment of the nuclear membrane to the nuclear lamina during cell division. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Apr 2016]

TOR1AIP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 1-179917990-G-A is Benign according to our data. Variant chr1-179917990-G-A is described in ClinVar as [Benign]. Clinvar id is 257698.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-179917990-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.014 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TOR1AIP1	NM_015602.4 linkuse as main transcript	c.1503G>A	p.Ala501=	synonymous_variant	10/10	ENST00000606911.7	NP_056417.2
TOR1AIP1	NM_001267578.2 linkuse as main transcript	c.1506G>A	p.Ala502=	synonymous_variant	10/10		NP_001254507.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TOR1AIP1	ENST00000606911.7 linkuse as main transcript	c.1503G>A	p.Ala501=	synonymous_variant	10/10	1	NM_015602.4	ENSP00000476687	P4	Q5JTV8-1

Frequencies

GnomAD3 genomes

AF:

0.932

AC:

141871

AN:

152154

Hom.:

66244

Cov.:

show subpopulations

Gnomad AFR

AF:

0.876

Gnomad AMI

AF:

0.987

Gnomad AMR

AF:

0.948

Gnomad ASJ

AF:

0.954

Gnomad EAS

AF:

0.905

Gnomad SAS

AF:

0.953

Gnomad FIN

AF:

0.981

Gnomad MID

AF:

0.962

Gnomad NFE

AF:

0.955

Gnomad OTH

AF:

0.928

GnomAD3 exomes

AF:

0.950

AC:

238682

AN:

251342

Hom.:

113448

AF XY:

0.951

AC XY:

129221

AN XY:

135840

show subpopulations

Gnomad AFR exome

AF:

0.875

Gnomad AMR exome

AF:

0.962

Gnomad ASJ exome

AF:

0.957

Gnomad EAS exome

AF:

0.900

Gnomad SAS exome

AF:

0.957

Gnomad FIN exome

AF:

0.979

Gnomad NFE exome

AF:

0.956

Gnomad OTH exome

AF:

0.956

GnomAD4 exome

AF:

0.952

AC:

1391452

AN:

1461894

Hom.:

662548

Cov.:

AF XY:

0.952

AC XY:

692399

AN XY:

727248

show subpopulations

Gnomad4 AFR exome

AF:

0.869

Gnomad4 AMR exome

AF:

0.961

Gnomad4 ASJ exome

AF:

0.957

Gnomad4 EAS exome

AF:

0.900

Gnomad4 SAS exome

AF:

0.956

Gnomad4 FIN exome

AF:

0.979

Gnomad4 NFE exome

AF:

0.954

Gnomad4 OTH exome

AF:

0.948

GnomAD4 genome

AF:

0.932

AC:

141977

AN:

152272

Hom.:

66292

Cov.:

AF XY:

0.933

AC XY:

69488

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.876

Gnomad4 AMR

AF:

0.948

Gnomad4 ASJ

AF:

0.954

Gnomad4 EAS

AF:

0.905

Gnomad4 SAS

AF:

0.952

Gnomad4 FIN

AF:

0.981

Gnomad4 NFE

AF:

0.955

Gnomad4 OTH

AF:

0.929

Alfa

AF:

0.948

Hom.:

55968

Bravo

AF:

0.926

Asia WGS

AF:

0.931

AC:

3238

AN:

3478

EpiCase

AF:

0.952

EpiControl

AF:

0.955

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Autosomal recessive limb-girdle muscular dystrophy type 2Y

Benign:2

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Apr 11, 2023	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 05, 2018	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

8.7

DANN

Benign

0.63

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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