rs1325268

Positions:

• chr1-66695298-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000371037.9(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 ENST00000371037.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.44

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 -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SGIP1	NM_032291.4	c.1571-136C>T		intron_variant		ENST00000371037.9	NP_115667.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SGIP1	ENST00000371037.9	c.1571-136C>T		intron_variant		1	NM_032291.4	ENSP00000360076

Frequencies

GnomAD3 genomes AF: 0.286 AC: 41711 AN: 145822 Hom.: 6116 Cov.: 27

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.: 30 AF XY: 0.301 AC XY: 188803 AN XY: 627374

Gnomad4 AFR exome AF: 0.260

Gnomad4 AMR exome AF: 0.290

Gnomad4 ASJ exome AF: 0.212

Gnomad4 EAS exome AF: 0.244

Gnomad4 SAS exome AF: 0.338

Gnomad4 FIN exome AF: 0.270

Gnomad4 NFE exome AF: 0.304

Gnomad4 OTH exome AF: 0.292

GnomAD4 genome AF: 0.286 AC: 41721 AN: 145908 Hom.: 6117 Cov.: 27 AF XY: 0.282 AC XY: 20005 AN XY: 70942

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.301

Alfa AF: 0.296 Hom.: 2308

Bravo AF: 0.288

Asia WGS AF: 0.249 AC: 865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	19
DANN	Benign	0.91

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

Other links and lift over

dbSNP: rs1325268; hg19: chr1-67160981; COSMIC: COSV52763189; COSMIC: COSV52763189;