rs6588207

Positions:

• chr1-66600872-A-G

Variant summary

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

The ENST00000371037.9(SGIP1):​c.11-24975A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 151,976 control chromosomes in the GnomAD database, including 30,431 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 0.62 (30431 hom., cov: 32)
• Consequence: SGIP1 ENST00000371037.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540

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]

LOC124904196 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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	Protein	UniProt
SGIP1	NM_032291.4	c.11-24975A>G		intron_variant		ENST00000371037.9	NP_115667.2
LOC124904196	XR_007066156.1	n.7158A>G		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SGIP1	ENST00000371037.9	c.11-24975A>G		intron_variant		1	NM_032291.4	ENSP00000360076

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94828 AN: 151858 Hom.: 30410 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.624 AC: 94901 AN: 151976 Hom.: 30431 Cov.: 32 AF XY: 0.627 AC XY: 46621 AN XY: 74314

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.886

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.623

Alfa AF: 0.592 Hom.: 54078

Bravo AF: 0.635

Asia WGS AF: 0.917 AC: 3189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.44

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: rs6588207; hg19: chr1-67066555;