11-90656697-C-T

Position:

• chr11-90656697-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000562245.5(DISC1FP1):​n.332+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 ENST00000562245.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210

Genes affected

DISC1FP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
DISC1FP1	NR_104190.1	n.332+53789C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DISC1FP1	ENST00000561596.5	n.279+53789C>T		intron_variant		5
DISC1FP1	ENST00000562245.5	n.332+53789C>T		intron_variant		3
DISC1FP1	ENST00000562678.5	n.185+109802C>T		intron_variant		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

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.290

Alfa AF: 0.263 Hom.: 7337

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2155076; hg19: chr11-90389865;