3-159541502-T-C

Position:

• chr3-159541502-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_014575.4(SCHIP1):​c.64-222941T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,028 control chromosomes in the GnomAD database, including 2,540 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 0.17 (2540 hom., cov: 32)
• Consequence: SCHIP1 NM_014575.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.588

Genes affected

SCHIP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCHIP1	NM_014575.4	c.64-222941T>C		intron_variant		ENST00000638749.2	NP_055390.1
IQCJ-SCHIP1	NM_001197113.2	c.292-222941T>C		intron_variant			NP_001184042.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26425 AN: 151910 Hom.: 2541 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.174 AC: 26436 AN: 152028 Hom.: 2540 Cov.: 32 AF XY: 0.182 AC XY: 13534 AN XY: 74290

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.175

Alfa AF: 0.175 Hom.: 3199

Bravo AF: 0.165

Asia WGS AF: 0.346 AC: 1203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	15
DANN	Benign	0.76

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: rs2222328; hg19: chr3-159259291;