ENST00000561596.5:n.33+9117G>A

Variant names:

• chr11-90260434-G-A
• rs10765288
• ENST00000561596.5:n.33+9117G>A

Variant summary

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

The ENST00000561596.5(DISC1FP1):​n.33+9117G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 151,940 control chromosomes in the GnomAD database, including 5,773 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 0.26 (5773 hom., cov: 32)
• Consequence: DISC1FP1 ENST00000561596.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DISC1FP1	NR_104190.1	n.86+9117G>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DISC1FP1	ENST00000561596.5	n.33+9117G>A		intron_variant	Intron 1 of 6	5
DISC1FP1	ENST00000562245.6	n.86+9117G>A		intron_variant	Intron 1 of 6	3
DISC1FP1	ENST00000649150.1	n.114+9117G>A		intron_variant	Intron 1 of 7
DISC1FP1	ENST00000745652.1	n.114+9117G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40135 AN: 151822 Hom.: 5764 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.264 AC: 40183 AN: 151940 Hom.: 5773 Cov.: 32 AF XY: 0.269 AC XY: 19947 AN XY: 74264

African (AFR) AF: 0.346 AC: 14335 AN: 41456

American (AMR) AF: 0.309 AC: 4708 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 590 AN: 3462

East Asian (EAS) AF: 0.417 AC: 2156 AN: 5174

South Asian (SAS) AF: 0.256 AC: 1232 AN: 4814

European-Finnish (FIN) AF: 0.262 AC: 2759 AN: 10550

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13661 AN: 67926

Other (OTH) AF: 0.250 AC: 529 AN: 2116

Alfa AF: 0.243 Hom.: 749

Bravo AF: 0.275

Asia WGS AF: 0.294 AC: 1023 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.29
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs10765288; hg19: chr11-89993602;