rs604737

chr1-66743405-G-A

Variant summary

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

The NM_032291.4(SGIP1):c.*310G>A variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.187 in 238,498 control chromosomes in the GnomAD database, including 5,048 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 0.18 (3038 hom., cov: 32)
  • Exomes 𝑓: 0.19 (2010 hom.)
• Consequence: SGIP1 NM_032291.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.21

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=-0.39).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SGIP1	NM_032291.4	c.*310G>A		3_prime_UTR_variant	25/25	ENST00000371037.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGIP1	ENST00000371037.9	c.*310G>A		3_prime_UTR_variant	25/25	1	NM_032291.4

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27781 AN: 152020 Hom.: 3038 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0796

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.144

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.192

GnomAD4 exome AF: 0.194 AC: 16759 AN: 86360 Hom.: 2010 Cov.: 0 AF XY: 0.182 AC XY: 8333 AN XY: 45692

Gnomad4 AFR exome AF: 0.110

Gnomad4 AMR exome AF: 0.117

Gnomad4 ASJ exome AF: 0.172

Gnomad4 EAS exome AF: 0.000996

Gnomad4 SAS exome AF: 0.0788

Gnomad4 FIN exome AF: 0.293

Gnomad4 NFE exome AF: 0.239

Gnomad4 OTH exome AF: 0.199

GnomAD4 genome AF: 0.183 AC: 27775 AN: 152138 Hom.: 3038 Cov.: 32 AF XY: 0.182 AC XY: 13560 AN XY: 74368

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0788

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.190

Alfa AF: 0.225 Hom.: 8226

Bravo AF: 0.167

Asia WGS AF: 0.0460 AC: 160 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
Cadd	Benign	14
Dann	Benign	0.84

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: rs604737; hg19: chr1-67209088; COSMIC: COSV52765160;