11-90509481-G-T

Variant names:

• chr11-90509481-G-T
• rs493622
• ENST00000561596.5:n.34-37273G>T

Variant summary

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

The ENST00000562245.6(DISC1FP1):​n.87-37273G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 151,694 control chromosomes in the GnomAD database, including 31,977 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 0.65 (31977 hom., cov: 32)
• Consequence: DISC1FP1 ENST00000562245.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562245.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DISC1FP1	NR_104190.1		n.87-37273G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DISC1FP1	ENST00000561596.5	TSL:5	n.34-37273G>T		intron	N/A
	DISC1FP1	ENST00000562245.6	TSL:3	n.87-37273G>T		intron	N/A
	DISC1FP1	ENST00000562678.5	TSL:3	n.43+20129G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98187 AN: 151576 Hom.: 31950 Cov.: 32

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.648 AC: 98268 AN: 151694 Hom.: 31977 Cov.: 32 AF XY: 0.652 AC XY: 48317 AN XY: 74138

African (AFR) AF: 0.640 AC: 26494 AN: 41400

American (AMR) AF: 0.729 AC: 11074 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2087 AN: 3468

East Asian (EAS) AF: 0.743 AC: 3800 AN: 5112

South Asian (SAS) AF: 0.752 AC: 3629 AN: 4826

European-Finnish (FIN) AF: 0.633 AC: 6690 AN: 10572

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42267 AN: 67820

Other (OTH) AF: 0.665 AC: 1402 AN: 2108

Alfa AF: 0.635 Hom.: 11936

Bravo AF: 0.650

Asia WGS AF: 0.757 AC: 2631 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.53
PhyloP100		0.075

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs493622;

hg19: chr11-90242649;