ENST00000561596.5:n.376+3228T>A

Variant names:

• chr11-90805090-T-A
• rs1404532
• ENST00000561596.5:n.376+3228T>A

Variant summary

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

The ENST00000561596.5(DISC1FP1):​n.376+3228T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 151,572 control chromosomes in the GnomAD database, including 22,634 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 0.54 (22634 hom., cov: 30)
• Consequence: DISC1FP1 ENST00000561596.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DISC1FP1	NR_104190.1	n.429+3228T>A		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DISC1FP1	ENST00000561596.5	n.376+3228T>A		intron_variant	Intron 4 of 6	5
DISC1FP1	ENST00000562245.5	n.429+3228T>A		intron_variant	Intron 4 of 6	3
DISC1FP1	ENST00000562678.5	n.282+3228T>A		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes AF: 0.541 AC: 81953 AN: 151454 Hom.: 22596 Cov.: 30

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.541 AC: 82058 AN: 151572 Hom.: 22634 Cov.: 30 AF XY: 0.553 AC XY: 40922 AN XY: 74034

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.559

Alfa AF: 0.397 Hom.: 1105

Bravo AF: 0.537

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1404532; hg19: chr11-90538258;