dbSNP rs1325268: SGIP1:c.1571-136C>T (chr1-66695298-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_032291.4(SGIP1):c.1571-136C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 1,429,936 control chromosomes in the GnomAD database, including 65,259 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 0.29 ( 6117 hom., cov: 27)

Exomes 𝑓: 0.30 ( 59142 hom. )

Consequence

SGIP1
NM_032291.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.44

Publications

6 publications found

Variant links:

Genes affected

SGIP1 (HGNC:25412): (SH3GL interacting endocytic adaptor 1) SGIP1 functions as an endocytic protein that affects signaling by receptors in neuronal systems involved in energy homeostasis via its interaction with endophilins (see SH3GL3; MIM 603362) (Trevaskis et al., 2005 [PubMed 15919751] and Uezu et al., 2007 [PubMed 17626015]).[supplied by OMIM, Mar 2008]

SGIP1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.35).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032291.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SGIP1	NM_032291.4	MANE Select	c.1571-136C>T	intron	N/A	NP_115667.2	Q9BQI5-1
SGIP1	NM_001350217.2		c.1583-136C>T	intron	N/A	NP_001337146.1	Q9BQI5-2
SGIP1	NM_001376534.1		c.1571-136C>T	intron	N/A	NP_001363463.1	Q9BQI5-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SGIP1	ENST00000371037.9	TSL:1 MANE Select	c.1571-136C>T	intron	N/A	ENSP00000360076.3	Q9BQI5-1
SGIP1	ENST00000371039.5	TSL:1	c.1039+794C>T	intron	N/A	ENSP00000360078.1	Q9BQI5-5
SGIP1	ENST00000237247.10	TSL:5	c.1664-136C>T	intron	N/A	ENSP00000237247.6	Q9BQI5-3

Frequencies

GnomAD3 genomes

AF:

0.286

AC:

41711

AN:

145822

Hom.:

6116

Cov.:

show subpopulations

Gnomad AFR

AF:

0.262

Gnomad AMI

AF:

0.337

Gnomad AMR

AF:

0.309

Gnomad ASJ

AF:

0.216

Gnomad EAS

AF:

0.211

Gnomad SAS

AF:

0.324

Gnomad FIN

AF:

0.259

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.304

Gnomad OTH

AF:

0.304

GnomAD4 exome

AF:

0.300

AC:

385077

AN:

1284028

Hom.:

59142

Cov.:

AF XY:

0.301

AC XY:

188803

AN XY:

627374

show subpopulations

African (AFR)

AF:

0.260

AC:

6990

AN:

26834

American (AMR)

AF:

0.290

AC:

6893

AN:

23800

Ashkenazi Jewish (ASJ)

AF:

0.212

AC:

4568

AN:

21582

East Asian (EAS)

AF:

0.244

AC:

7363

AN:

30224

South Asian (SAS)

AF:

0.338

AC:

18554

AN:

54942

European-Finnish (FIN)

AF:

0.270

AC:

12862

AN:

47664

Middle Eastern (MID)

AF:

0.312

AC:

1598

AN:

5130

European-Non Finnish (NFE)

AF:

0.304

AC:

310868

AN:

1021126

Other (OTH)

AF:

0.292

AC:

15381

AN:

52726

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

11712

23424

35136

46848

58560

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10722

21444

32166

42888

53610

<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:

0.286

AC:

41721

AN:

145908

Hom.:

6117

Cov.:

AF XY:

0.282

AC XY:

20005

AN XY:

70942

show subpopulations

African (AFR)

AF:

0.262

AC:

10249

AN:

39088

American (AMR)

AF:

0.308

AC:

4529

AN:

14682

Ashkenazi Jewish (ASJ)

AF:

0.216

AC:

736

AN:

3404

East Asian (EAS)

AF:

0.212

AC:

1038

AN:

4904

South Asian (SAS)

AF:

0.323

AC:

1457

AN:

4504

European-Finnish (FIN)

AF:

0.259

AC:

2422

AN:

9364

Middle Eastern (MID)

AF:

0.278

AC:

AN:

284

European-Non Finnish (NFE)

AF:

0.304

AC:

20295

AN:

66740

Other (OTH)

AF:

0.301

AC:

613

AN:

2038

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

1329

2659

3988

5318

6647

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

418

836

1254

1672

2090

<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:

0.295

Hom.:

3426

Bravo

AF:

0.288

Asia WGS

AF:

0.249

AC:

865

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.35

CADD

Benign

(source)

DANN

Benign

0.91

PhyloP100

3.4

Mutation Taster

=293/7

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over