ENST00000561596.5:n.34-125109A>G

Variant names:

• chr11-90421645-A-G
• rs1354913
• ENST00000561596.5:n.34-125109A>G

Variant summary

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

The ENST00000561596.5(DISC1FP1):​n.34-125109A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,032 control chromosomes in the GnomAD database, including 3,542 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 0.20 (3542 hom., cov: 32)
• Consequence: DISC1FP1 ENST00000561596.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 1 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.453 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.87-125109A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DISC1FP1	ENST00000561596.5	TSL:5	n.34-125109A>G		intron	N/A
	DISC1FP1	ENST00000562245.6	TSL:3	n.87-125109A>G		intron	N/A
	DISC1FP1	ENST00000649150.1		n.178+60023A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30695 AN: 151914 Hom.: 3529 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.202 AC: 30727 AN: 152032 Hom.: 3542 Cov.: 32 AF XY: 0.207 AC XY: 15402 AN XY: 74294

African (AFR) AF: 0.147 AC: 6094 AN: 41502

American (AMR) AF: 0.263 AC: 4011 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3470

East Asian (EAS) AF: 0.469 AC: 2424 AN: 5170

South Asian (SAS) AF: 0.277 AC: 1329 AN: 4806

European-Finnish (FIN) AF: 0.264 AC: 2783 AN: 10554

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.190 AC: 12901 AN: 67934

Other (OTH) AF: 0.206 AC: 435 AN: 2112

Alfa AF: 0.198 Hom.: 1911

Bravo AF: 0.202

Asia WGS AF: 0.311 AC: 1078 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.52
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1354913; hg19: chr11-90154813;