GeneBe

rs1127460

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001367651.1(SUN1):​c.485+144T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 34)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

SUN1
NM_001367651.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0850

Publications

7 publications found
Variant links:
Genes affected
SUN1 (HGNC:18587): (Sad1 and UNC84 domain containing 1) This gene is a member of the unc-84 homolog family and encodes a nuclear envelope protein with an Unc84 (SUN) domain. The protein is involved in nuclear anchorage and migration. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2019]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367651.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SUN1
NM_001130965.3
MANE Select
c.266+144T>A
intron
N/ANP_001124437.1
SUN1
NM_001367651.1
c.485+144T>A
intron
N/ANP_001354580.1
SUN1
NM_001367705.1
c.266+144T>A
intron
N/ANP_001354634.1

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SUN1
ENST00000401592.6
TSL:1 MANE Select
c.266+144T>A
intron
N/AENSP00000384015.1
SUN1
ENST00000457378.6
TSL:1
c.329+144T>A
intron
N/AENSP00000395952.2
SUN1
ENST00000963118.1
c.266+144T>A
intron
N/AENSP00000633177.1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
152182
Hom.:
0
Cov.:
34
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
560802
Hom.:
0
Cov.:
8
AF XY:
0.00
AC XY:
0
AN XY:
280400
African (AFR)
AF:
0.00
AC:
0
AN:
13564
American (AMR)
AF:
0.00
AC:
0
AN:
10458
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
12576
East Asian (EAS)
AF:
0.00
AC:
0
AN:
26184
South Asian (SAS)
AF:
0.00
AC:
0
AN:
23896
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
24810
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2006
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
419350
Other (OTH)
AF:
0.00
AC:
0
AN:
27958
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
152182
Hom.:
0
Cov.:
34
AF XY:
0.00
AC XY:
0
AN XY:
74346
African (AFR)
AF:
0.00
AC:
0
AN:
41422
American (AMR)
AF:
0.00
AC:
0
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3472
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5200
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4830
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10616
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
68032
Other (OTH)
AF:
0.00
AC:
0
AN:
2094

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.9
DANN
Benign
0.56
PhyloP100
-0.085
PromoterAI
-0.011
Neutral

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

Other links and lift over

dbSNP: rs1127460; hg19: chr7-878767; API