11-90289118-G-C

Variant names:

• chr11-90289118-G-C
• rs10501718
• ENST00000561596.5:n.33+37801G>C

Variant summary

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

The ENST00000562245.6(DISC1FP1):​n.86+37801G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0516 in 152,158 control chromosomes in the GnomAD database, including 478 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 0.052 (478 hom., cov: 32)
• Consequence: DISC1FP1 ENST00000562245.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.868
• 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=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 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.86+37801G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DISC1FP1	ENST00000561596.5	TSL:5	n.33+37801G>C		intron	N/A
	DISC1FP1	ENST00000562245.6	TSL:3	n.86+37801G>C		intron	N/A
	DISC1FP1	ENST00000649150.1		n.114+37801G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0516 AC: 7838 AN: 152038 Hom.: 477 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0226

Gnomad ASJ AF: 0.0418

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00290

Gnomad FIN AF: 0.00501

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0164

Gnomad OTH AF: 0.0393

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

GnomAD4 genome AF: 0.0516 AC: 7852 AN: 152158 Hom.: 478 Cov.: 32 AF XY: 0.0487 AC XY: 3624 AN XY: 74392

African (AFR) AF: 0.147 AC: 6091 AN: 41488

American (AMR) AF: 0.0226 AC: 345 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0418 AC: 145 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.00290 AC: 14 AN: 4830

European-Finnish (FIN) AF: 0.00501 AC: 53 AN: 10584

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0164 AC: 1112 AN: 68004

Other (OTH) AF: 0.0389 AC: 82 AN: 2110

Alfa AF: 0.0394 Hom.: 39

Bravo AF: 0.0579

Asia WGS AF: 0.00982 AC: 35 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	19
DANN	Benign	0.74
PhyloP100		0.87

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: rs10501718;

hg19: chr11-90022286;