rs6588207

Variant names:

• chr1-66600872-A-G
• rs6588207
• NM_032291.4:c.11-24975A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032291.4(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 NM_032291.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032291.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SGIP1	NM_032291.4	MANE Select	c.11-24975A>G		intron	N/A	NP_115667.2	Q9BQI5-1
	SGIP1	NM_001350217.2		c.11-24975A>G		intron	N/A	NP_001337146.1	Q9BQI5-2
	SGIP1	NM_001376534.1		c.11-24975A>G		intron	N/A	NP_001363463.1	Q9BQI5-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SGIP1	ENST00000371037.9	TSL:1 MANE Select	c.11-24975A>G		intron	N/A	ENSP00000360076.3	Q9BQI5-1
	SGIP1	ENST00000371039.5	TSL:1	c.11-24975A>G		intron	N/A	ENSP00000360078.1	Q9BQI5-5
	SGIP1	ENST00000237247.10	TSL:5	c.11-24975A>G		intron	N/A	ENSP00000237247.6	Q9BQI5-3

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

African (AFR) AF: 0.629 AC: 26065 AN: 41418

American (AMR) AF: 0.712 AC: 10870 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2144 AN: 3466

East Asian (EAS) AF: 0.998 AC: 5170 AN: 5178

South Asian (SAS) AF: 0.886 AC: 4278 AN: 4830

European-Finnish (FIN) AF: 0.518 AC: 5466 AN: 10562

Middle Eastern (MID) AF: 0.634 AC: 185 AN: 292

European-Non Finnish (NFE) AF: 0.572 AC: 38840 AN: 67944

Other (OTH) AF: 0.623 AC: 1313 AN: 2106

Alfa AF: 0.597 Hom.: 86331

Bravo AF: 0.635

Asia WGS AF: 0.917 AC: 3189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.44
PhyloP100		-0.054
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6588207; hg19: chr1-67066555;