rs660753

Positions:

• chr11-90639135-G-A
• chr11-90639135-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.332+36227G>A 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 0.481 in 151,924 control chromosomes in the GnomAD database, including 18,426 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 0.48 (18426 hom., cov: 32)
• Consequence: DISC1FP1 NR_104190.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DISC1FP1	NR_104190.1	n.332+36227G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DISC1FP1	ENST00000649150.1	n.320+92240G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73087 AN: 151806 Hom.: 18428 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.481 AC: 73105 AN: 151924 Hom.: 18426 Cov.: 32 AF XY: 0.481 AC XY: 35728 AN XY: 74276

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.501

Alfa AF: 0.535 Hom.: 12757

Bravo AF: 0.470

Asia WGS AF: 0.620 AC: 2154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.95
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs660753; hg19: chr11-90372303;