3-159780660-C-G

Position:

• chr3-159780660-C-G

Variant summary

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

The NM_014575.4(SCHIP1):​c.759+15522C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,122 control chromosomes in the GnomAD database, including 45,262 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 0.76 (45262 hom., cov: 32)
• Consequence: SCHIP1 NM_014575.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299

Genes affected

SCHIP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCHIP1	NM_014575.4	c.759+15522C>G		intron_variant		ENST00000638749.2
IQCJ-SCHIP1	NM_001197113.2	c.987+15522C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115660 AN: 152004 Hom.: 45210 Cov.: 32

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.761 AC: 115767 AN: 152122 Hom.: 45262 Cov.: 32 AF XY: 0.763 AC XY: 56746 AN XY: 74356

Gnomad4 AFR AF: 0.931

Gnomad4 AMR AF: 0.732

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.815

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.783

Alfa AF: 0.708 Hom.: 4862

Bravo AF: 0.771

Asia WGS AF: 0.916 AC: 3183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.74
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: rs2886623; hg19: chr3-159498449;