11-90643897-C-T

Variant names:

• chr11-90643897-C-T
• rs10501729
• ENST00000561596.5:n.279+40989C>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+40989C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0929 in 151,986 control chromosomes in the GnomAD database, including 698 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 0.093 (698 hom., cov: 32)
• Consequence: DISC1FP1 ENST00000561596.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DISC1FP1	NR_104190.1	n.332+40989C>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+40989C>T		intron_variant	Intron 3 of 6	5
DISC1FP1	ENST00000562245.6	n.332+40989C>T		intron_variant	Intron 3 of 6	3
DISC1FP1	ENST00000562678.5	n.185+97002C>T		intron_variant	Intron 2 of 5	3

Frequencies

GnomAD3 genomes AF: 0.0928 AC: 14100 AN: 151864 Hom.: 698 Cov.: 32

Gnomad AFR AF: 0.0914

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0833

Gnomad ASJ AF: 0.0853

Gnomad EAS AF: 0.0298

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0865

Gnomad NFE AF: 0.0993

Gnomad OTH AF: 0.0891

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

GnomAD4 genome AF: 0.0929 AC: 14113 AN: 151986 Hom.: 698 Cov.: 32 AF XY: 0.0912 AC XY: 6776 AN XY: 74266

African (AFR) AF: 0.0913 AC: 3788 AN: 41476

American (AMR) AF: 0.0832 AC: 1269 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0853 AC: 296 AN: 3470

East Asian (EAS) AF: 0.0303 AC: 156 AN: 5152

South Asian (SAS) AF: 0.108 AC: 519 AN: 4820

European-Finnish (FIN) AF: 0.103 AC: 1084 AN: 10536

Middle Eastern (MID) AF: 0.0856 AC: 25 AN: 292

European-Non Finnish (NFE) AF: 0.0994 AC: 6753 AN: 67958

Other (OTH) AF: 0.0882 AC: 186 AN: 2110

Alfa AF: 0.0973 Hom.: 2163

Bravo AF: 0.0922

Asia WGS AF: 0.0920 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.23
DANN	Benign	0.50
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10501729; hg19: chr11-90377065;