rs6656912

Variant names:

• chr1-66617988-T-C
• rs6656912
• NM_032291.4:c.11-7859T>C

Variant summary

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

The NM_032291.4(SGIP1):​c.11-7859T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,124 control chromosomes in the GnomAD database, including 38,927 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 0.70 (38927 hom., cov: 32)
• Consequence: SGIP1 NM_032291.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522
• Publications: 8 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• 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 rank	MANE	Protein	UniProt
SGIP1	NM_032291.4	c.11-7859T>C		intron_variant	Intron 1 of 24	ENST00000371037.9	NP_115667.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SGIP1	ENST00000371037.9	c.11-7859T>C		intron_variant	Intron 1 of 24	1	NM_032291.4	ENSP00000360076.3

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106302 AN: 152006 Hom.: 38866 Cov.: 32

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.922

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.700 AC: 106425 AN: 152124 Hom.: 38927 Cov.: 32 AF XY: 0.701 AC XY: 52123 AN XY: 74350

African (AFR) AF: 0.869 AC: 36096 AN: 41516

American (AMR) AF: 0.741 AC: 11323 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2261 AN: 3472

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

South Asian (SAS) AF: 0.921 AC: 4440 AN: 4822

European-Finnish (FIN) AF: 0.516 AC: 5455 AN: 10570

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.581 AC: 39468 AN: 67972

Other (OTH) AF: 0.684 AC: 1444 AN: 2112

Alfa AF: 0.633 Hom.: 15831

Bravo AF: 0.719

Asia WGS AF: 0.943 AC: 3279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.52
DANN	Benign	0.29
PhyloP100		-0.52
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: rs6656912; hg19: chr1-67083671;