11-90421645-A-G

Position:

• chr11-90421645-A-G

Variant summary

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

The NR_104190.1(DISC1FP1):​n.87-125109A>G 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 0.202 in 152,032 control chromosomes in the GnomAD database, including 3,542 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 0.20 (3542 hom., cov: 32)
• Consequence: DISC1FP1 NR_104190.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DISC1FP1	NR_104190.1	n.87-125109A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DISC1FP1	ENST00000649150.1	n.178+60023A>G		intron_variant, non_coding_transcript_variant
DISC1FP1	ENST00000561596.5	n.34-125109A>G		intron_variant, non_coding_transcript_variant		5
DISC1FP1	ENST00000562245.5	n.87-125109A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30695 AN: 151914 Hom.: 3529 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.202 AC: 30727 AN: 152032 Hom.: 3542 Cov.: 32 AF XY: 0.207 AC XY: 15402 AN XY: 74294

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.206

Alfa AF: 0.199 Hom.: 1776

Bravo AF: 0.202

Asia WGS AF: 0.311 AC: 1078 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1354913; hg19: chr11-90154813;