rs500737

Positions:

• chr11-90414281-G-C

Variant summary

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

The NR_104190.1(DISC1FP1):​n.87-132473G>C 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 0.649 in 150,626 control chromosomes in the GnomAD database, including 31,908 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 (31908 hom., cov: 27)
• Consequence: DISC1FP1 NR_104190.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690

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=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DISC1FP1	NR_104190.1	n.87-132473G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DISC1FP1	ENST00000649150.1	n.178+52659G>C		intron_variant, non_coding_transcript_variant
DISC1FP1	ENST00000561596.5	n.34-132473G>C		intron_variant, non_coding_transcript_variant		5
DISC1FP1	ENST00000562245.5	n.87-132473G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.648 AC: 97590 AN: 150506 Hom.: 31870 Cov.: 27

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.645

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.649 AC: 97687 AN: 150626 Hom.: 31908 Cov.: 27 AF XY: 0.651 AC XY: 47830 AN XY: 73518

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.651

Alfa AF: 0.643 Hom.: 3889

Bravo AF: 0.651

Asia WGS AF: 0.780 AC: 2711 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	0.20
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs500737; hg19: chr11-90147449;