chr11-90285120-A-C

Variant names:

• chr11-90285120-A-C
• rs12364205
• ENST00000561596.5:n.33+33803A>C

Variant summary

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

The ENST00000561596.5(DISC1FP1):​n.33+33803A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 152,012 control chromosomes in the GnomAD database, including 14,030 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 0.41 (14030 hom., cov: 32)
• Consequence: DISC1FP1 ENST00000561596.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43
• Publications: 1 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=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DISC1FP1	NR_104190.1	n.86+33803A>C		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DISC1FP1	ENST00000561596.5	n.33+33803A>C		intron_variant	Intron 1 of 6	5
DISC1FP1	ENST00000562245.6	n.86+33803A>C		intron_variant	Intron 1 of 6	3
DISC1FP1	ENST00000649150.1	n.114+33803A>C		intron_variant	Intron 1 of 7
DISC1FP1	ENST00000745652.1	n.114+33803A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62078 AN: 151894 Hom.: 14024 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.409 AC: 62111 AN: 152012 Hom.: 14030 Cov.: 32 AF XY: 0.407 AC XY: 30228 AN XY: 74310

African (AFR) AF: 0.215 AC: 8922 AN: 41476

American (AMR) AF: 0.397 AC: 6062 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1511 AN: 3470

East Asian (EAS) AF: 0.387 AC: 1998 AN: 5162

South Asian (SAS) AF: 0.389 AC: 1876 AN: 4818

European-Finnish (FIN) AF: 0.514 AC: 5425 AN: 10550

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.514 AC: 34936 AN: 67940

Other (OTH) AF: 0.402 AC: 848 AN: 2110

Alfa AF: 0.478 Hom.: 26128

Bravo AF: 0.394

Asia WGS AF: 0.360 AC: 1249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.5
DANN	Benign	0.93
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs12364205; hg19: chr11-90018288;