chr11-90656697-C-T

Variant names:

• chr11-90656697-C-T
• rs2155076
• ENST00000561596.5:n.279+53789C>T

Variant summary

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

The ENST00000561596.5(DISC1FP1):​n.279+53789C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,022 control chromosomes in the GnomAD database, including 7,470 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 0.30 (7470 hom., cov: 32)
• Consequence: DISC1FP1 ENST00000561596.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DISC1FP1	NR_104190.1	n.332+53789C>T		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DISC1FP1	ENST00000561596.5	n.279+53789C>T		intron_variant	Intron 3 of 6	5
DISC1FP1	ENST00000562245.6	n.332+53789C>T		intron_variant	Intron 3 of 6	3
DISC1FP1	ENST00000562678.5	n.185+109802C>T		intron_variant	Intron 2 of 5	3

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45495 AN: 151900 Hom.: 7463 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.299 AC: 45525 AN: 152022 Hom.: 7470 Cov.: 32 AF XY: 0.295 AC XY: 21887 AN XY: 74304

African (AFR) AF: 0.439 AC: 18191 AN: 41446

American (AMR) AF: 0.214 AC: 3268 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 820 AN: 3472

East Asian (EAS) AF: 0.326 AC: 1679 AN: 5158

South Asian (SAS) AF: 0.153 AC: 736 AN: 4822

European-Finnish (FIN) AF: 0.238 AC: 2524 AN: 10584

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17507 AN: 67964

Other (OTH) AF: 0.290 AC: 611 AN: 2110

Alfa AF: 0.268 Hom.: 9677

Bravo AF: 0.307

Asia WGS AF: 0.202 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.60
PhyloP100		-0.021

Splicing

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

Other links and lift over

dbSNP: rs2155076; hg19: chr11-90389865;