ENST00000561596.5:n.34-10102T>C

Variant names:

• chr11-90536652-T-C
• rs10830528
• ENST00000561596.5:n.34-10102T>C

Variant summary

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

The ENST00000561596.5(DISC1FP1):​n.34-10102T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,050 control chromosomes in the GnomAD database, including 3,772 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 0.21 (3772 hom., cov: 32)
• Consequence: DISC1FP1 ENST00000561596.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284
• Publications: 0 publications found

Genes affected

DISC1FP1 (HGNC:33625): (DISC1 fusion partner 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000561596.5. 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
	DISC1FP1	NR_104190.1		n.87-10102T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DISC1FP1	ENST00000561596.5	TSL:5	n.34-10102T>C		intron	N/A
	DISC1FP1	ENST00000562245.6	TSL:3	n.87-10102T>C		intron	N/A
	DISC1FP1	ENST00000562678.5	TSL:3	n.44-10102T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31467 AN: 151932 Hom.: 3754 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.207 AC: 31520 AN: 152050 Hom.: 3772 Cov.: 32 AF XY: 0.212 AC XY: 15739 AN XY: 74314

African (AFR) AF: 0.259 AC: 10740 AN: 41500

American (AMR) AF: 0.295 AC: 4495 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 391 AN: 3466

East Asian (EAS) AF: 0.456 AC: 2343 AN: 5142

South Asian (SAS) AF: 0.208 AC: 1004 AN: 4824

European-Finnish (FIN) AF: 0.213 AC: 2254 AN: 10576

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.141 AC: 9591 AN: 67966

Other (OTH) AF: 0.205 AC: 433 AN: 2114

Alfa AF: 0.178 Hom.: 349

Bravo AF: 0.220

Asia WGS AF: 0.282 AC: 981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.3
DANN	Benign	0.61
PhyloP100		-0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10830528; hg19: chr11-90269820;