NM_014575.4:c.64-68495C>T

Variant names:

• chr3-159695948-C-T
• rs9812406
• NM_014575.4:c.64-68495C>T

Variant summary

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

The NM_014575.4(SCHIP1):​c.64-68495C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 151,878 control chromosomes in the GnomAD database, including 9,415 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 0.29 (9415 hom., cov: 32)
• Consequence: SCHIP1 NM_014575.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818
• Publications: 7 publications found

Genes affected

SCHIP1 (HGNC:15678): (schwannomin interacting protein 1) Enables identical protein binding activity. Predicted to be involved in positive regulation of hippo signaling. Predicted to act upstream of or within several processes, including animal organ development; face morphogenesis; and fibroblast migration. Located in several cellular components, including cell junction; cytosol; and nuclear body. [provided by Alliance of Genome Resources, Apr 2022]

IQCJ-SCHIP1 (HGNC:38842): (IQCJ-SCHIP1 readthrough) This locus represents naturally occurring read-through transcription from the neighboring IQ motif containing J (IQCJ) and schwannomin interacting protein 1 (SCHIP1) genes. Alternative splicing results in multiple transcript variants that are composed of in-frame exons from each individual gene. The resulting fusion products are thought to be components of the multimolecular complexes of axon initial segments and nodes of Ranvier, and they may play a role in calcium-mediated responses. [provided by RefSeq, Oct 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014575.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCHIP1	NM_014575.4	MANE Select	c.64-68495C>T		intron	N/A	NP_055390.1
	IQCJ-SCHIP1	NM_001197113.2		c.292-68495C>T		intron	N/A	NP_001184042.1
	IQCJ-SCHIP1	NM_001197114.2		c.211-68495C>T		intron	N/A	NP_001184043.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCHIP1	ENST00000638749.2	TSL:1 MANE Select	c.64-68495C>T		intron	N/A	ENSP00000491030.1
	IQCJ-SCHIP1	ENST00000485419.7	TSL:2	c.292-68495C>T		intron	N/A	ENSP00000420182.1
	SCHIP1	ENST00000412423.8	TSL:1	c.64-68495C>T		intron	N/A	ENSP00000400942.2

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43883 AN: 151760 Hom.: 9370 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.290 AC: 43994 AN: 151878 Hom.: 9415 Cov.: 32 AF XY: 0.286 AC XY: 21222 AN XY: 74232

African (AFR) AF: 0.600 AC: 24806 AN: 41340

American (AMR) AF: 0.288 AC: 4404 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3462

East Asian (EAS) AF: 0.226 AC: 1164 AN: 5160

South Asian (SAS) AF: 0.227 AC: 1095 AN: 4822

European-Finnish (FIN) AF: 0.106 AC: 1116 AN: 10550

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9990 AN: 67966

Other (OTH) AF: 0.288 AC: 607 AN: 2110

Alfa AF: 0.191 Hom.: 16693

Bravo AF: 0.316

Asia WGS AF: 0.287 AC: 998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.64
PhyloP100		-0.82
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: rs9812406; hg19: chr3-159413737;