Genetic Variant NM_001040455.2:c.1016-32C>T (chr11-117187346-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001040455.2(SIDT2):c.1016-32C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0727 in 1,602,008 control chromosomes in the GnomAD database, including 5,904 homozygotes. 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 0.12 ( 1636 hom., cov: 31)

Exomes 𝑓: 0.068 ( 4268 hom. )

Consequence

SIDT2
NM_001040455.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.505

Publications

7 publications found

Variant links:

Genes affected

SIDT2 (HGNC:24272): (SID1 transmembrane family member 2) Predicted to enable several functions, including AP-1 adaptor complex binding activity; AP-2 adaptor complex binding activity; and RNA transmembrane transporter activity. Involved in RNA transport. Located in lysosomal membrane and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SIDT2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SIDT2	NM_001040455.2 link	c.1016-32C>T		intron_variant	Intron 10 of 25	ENST00000324225.9	NP_001035545.1	Q8NBJ9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SIDT2	ENST00000324225.9 link	c.1016-32C>T		intron_variant	Intron 10 of 25	1	NM_001040455.2	ENSP00000314023.4		Q8NBJ9-1

Frequencies

GnomAD3 genomes

AF:

0.118

AC:

17931

AN:

151928

Hom.:

1636

Cov.:

show subpopulations

Gnomad AFR

AF:

0.259

Gnomad AMI

AF:

0.00879

Gnomad AMR

AF:

0.0581

Gnomad ASJ

AF:

0.106

Gnomad EAS

AF:

0.0899

Gnomad SAS

AF:

0.0993

Gnomad FIN

AF:

0.0753

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.0589

Gnomad OTH

AF:

0.0977

GnomAD2 exomes

AF:

0.0821

AC:

20645

AN:

251406

AF XY:

0.0798

show subpopulations

Gnomad AFR exome

AF:

0.263

Gnomad AMR exome

AF:

0.0497

Gnomad ASJ exome

AF:

0.0986

Gnomad EAS exome

AF:

0.102

Gnomad FIN exome

AF:

0.0769

Gnomad NFE exome

AF:

0.0591

Gnomad OTH exome

AF:

0.0701

GnomAD4 exome

AF:

0.0680

AC:

98555

AN:

1449962

Hom.:

4268

Cov.:

AF XY:

0.0682

AC XY:

49239

AN XY:

722032

show subpopulations

African (AFR)

AF:

0.263

AC:

8755

AN:

33228

American (AMR)

AF:

0.0525

AC:

2345

AN:

44700

Ashkenazi Jewish (ASJ)

AF:

0.0985

AC:

2569

AN:

26070

East Asian (EAS)

AF:

0.103

AC:

4080

AN:

39642

South Asian (SAS)

AF:

0.0929

AC:

7988

AN:

86028

European-Finnish (FIN)

AF:

0.0750

AC:

4006

AN:

53418

Middle Eastern (MID)

AF:

0.117

AC:

669

AN:

5738

European-Non Finnish (NFE)

AF:

0.0576

AC:

63442

AN:

1101138

Other (OTH)

AF:

0.0784

AC:

4701

AN:

60000

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

4918

9837

14755

19674

24592

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2548

5096

7644

10192

12740

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.118

AC:

17927

AN:

152046

Hom.:

1636

Cov.:

AF XY:

0.117

AC XY:

8689

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.258

AC:

10690

AN:

41408

American (AMR)

AF:

0.0579

AC:

885

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.106

AC:

367

AN:

3466

East Asian (EAS)

AF:

0.0893

AC:

462

AN:

5172

South Asian (SAS)

AF:

0.0985

AC:

475

AN:

4822

European-Finnish (FIN)

AF:

0.0753

AC:

797

AN:

10590

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0589

AC:

4005

AN:

67990

Other (OTH)

AF:

0.0962

AC:

203

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

733

1466

2198

2931

3664

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

190

380

570

760

950

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0954

Hom.:

249

Bravo

AF:

0.125

Asia WGS

AF:

0.0960

AC:

339

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

8.2

(source)

DANN

Benign

0.56

PhyloP100

-0.51

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over