rs10789215

chr1-66685502-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032291.4(SGIP1):c.1315+3133T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 152,028 control chromosomes in the GnomAD database, including 35,740 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 0.67 (35740 hom., cov: 32)
• Consequence: SGIP1 NM_032291.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SGIP1	NM_032291.4	c.1315+3133T>C		intron_variant		ENST00000371037.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGIP1	ENST00000371037.9	c.1315+3133T>C		intron_variant		1	NM_032291.4

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102320 AN: 151910 Hom.: 35690 Cov.: 32

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.649

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.674 AC: 102434 AN: 152028 Hom.: 35740 Cov.: 32 AF XY: 0.676 AC XY: 50282 AN XY: 74336

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.732

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.889

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.653

Alfa AF: 0.607 Hom.: 38805

Bravo AF: 0.689

Asia WGS AF: 0.926 AC: 3219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.11
Dann	Benign	0.35

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs10789215; hg19: chr1-67151185;