1-66566224-T-G

Position:

• chr1-66566224-T-G

Variant summary

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

The NM_032291.4(SGIP1):​c.10+31856T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 151,712 control chromosomes in the GnomAD database, including 19,171 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 0.49 (19171 hom., cov: 32)
• Consequence: SGIP1 NM_032291.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191

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]

SGIP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SGIP1	NM_032291.4	c.10+31856T>G		intron_variant		ENST00000371037.9	NP_115667.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SGIP1	ENST00000371037.9	c.10+31856T>G		intron_variant		1	NM_032291.4	ENSP00000360076.3

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74832 AN: 151596 Hom.: 19151 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.494 AC: 74896 AN: 151712 Hom.: 19171 Cov.: 32 AF XY: 0.495 AC XY: 36671 AN XY: 74122

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.680

Gnomad4 SAS AF: 0.778

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.512

Alfa AF: 0.466 Hom.: 2651

Bravo AF: 0.501

Asia WGS AF: 0.731 AC: 2538 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.38

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: rs7537440; hg19: chr1-67031907;