chr3-159541669-T-C

Position:

• chr3-159541669-T-C

Variant summary

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

The NM_014575.4(SCHIP1):​c.64-222774T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,906 control chromosomes in the GnomAD database, including 8,675 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 0.33 (8675 hom., cov: 32)
• Consequence: SCHIP1 NM_014575.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518

Genes affected

SCHIP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCHIP1	NM_014575.4	c.64-222774T>C		intron_variant		ENST00000638749.2
IQCJ-SCHIP1	NM_001197113.2	c.292-222774T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50759 AN: 151788 Hom.: 8649 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.335 AC: 50822 AN: 151906 Hom.: 8675 Cov.: 32 AF XY: 0.342 AC XY: 25358 AN XY: 74230

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.332

Alfa AF: 0.312 Hom.: 4229

Bravo AF: 0.329

Asia WGS AF: 0.527 AC: 1831 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.84

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: rs1402276; hg19: chr3-159259458;