chr11-90509481-G-T

Position:

• chr11-90509481-G-T

Variant summary

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

The NR_104190.1(DISC1FP1):​n.87-37273G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 151,694 control chromosomes in the GnomAD database, including 31,977 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 0.65 (31977 hom., cov: 32)
• Consequence: DISC1FP1 NR_104190.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750

Genes affected

DISC1FP1 (HGNC:33625): (DISC1 fusion partner 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DISC1FP1	NR_104190.1	n.87-37273G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DISC1FP1	ENST00000649150.1	n.179-37273G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98187 AN: 151576 Hom.: 31950 Cov.: 32

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.648 AC: 98268 AN: 151694 Hom.: 31977 Cov.: 32 AF XY: 0.652 AC XY: 48317 AN XY: 74138

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.729

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.665

Alfa AF: 0.635 Hom.: 7501

Bravo AF: 0.650

Asia WGS AF: 0.757 AC: 2631 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs493622; hg19: chr11-90242649;