11-90549864-C-T

Variant names:

• chr11-90549864-C-T
• rs10501723
• ENST00000561596.5:n.175+2969C>T

Variant summary

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

The ENST00000562245.6(DISC1FP1):​n.228+2969C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 151,962 control chromosomes in the GnomAD database, including 15,847 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 0.45 (15847 hom., cov: 32)
• Consequence: DISC1FP1 ENST00000562245.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.527 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.228+2969C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DISC1FP1	ENST00000561596.5	TSL:5	n.175+2969C>T		intron	N/A
	DISC1FP1	ENST00000562245.6	TSL:3	n.228+2969C>T		intron	N/A
	DISC1FP1	ENST00000562678.5	TSL:3	n.185+2969C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68938 AN: 151844 Hom.: 15842 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.454 AC: 68969 AN: 151962 Hom.: 15847 Cov.: 32 AF XY: 0.452 AC XY: 33582 AN XY: 74256

African (AFR) AF: 0.429 AC: 17791 AN: 41426

American (AMR) AF: 0.440 AC: 6721 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1703 AN: 3470

East Asian (EAS) AF: 0.287 AC: 1477 AN: 5154

South Asian (SAS) AF: 0.544 AC: 2624 AN: 4824

European-Finnish (FIN) AF: 0.418 AC: 4413 AN: 10562

Middle Eastern (MID) AF: 0.459 AC: 134 AN: 292

European-Non Finnish (NFE) AF: 0.481 AC: 32717 AN: 67954

Other (OTH) AF: 0.463 AC: 977 AN: 2112

Alfa AF: 0.456 Hom.: 9752

Bravo AF: 0.447

Asia WGS AF: 0.479 AC: 1666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.72
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs10501723; hg19: chr11-90283032;