rs2916

Positions:

• chr1-66751014-G-A

Variant summary

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

The NM_032291.4(SGIP1):​c.*7919G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,002 control chromosomes in the GnomAD database, including 10,859 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 0.36 (10859 hom., cov: 32)
• Consequence: SGIP1 NM_032291.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.736

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SGIP1	NM_032291.4	c.*7919G>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.*7919G>A		3_prime_UTR_variant	25/25	1	NM_032291.4

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55292 AN: 151884 Hom.: 10860 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.00481

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.364 AC: 55322 AN: 152002 Hom.: 10859 Cov.: 32 AF XY: 0.360 AC XY: 26772 AN XY: 74292

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.00482

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.364

Alfa AF: 0.396 Hom.: 15618

Bravo AF: 0.354

Asia WGS AF: 0.110 AC: 384 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.3
DANN	Benign	0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2916; hg19: chr1-67216697; COSMIC: COSV51075252;