rs500737

Variant names:

• chr11-90414281-G-C
• rs500737
• ENST00000561596.5:n.34-132473G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000561596.5(DISC1FP1):​n.34-132473G>C variant causes a intron 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 ENST00000561596.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000561596.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DISC1FP1	NR_104190.1		n.87-132473G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DISC1FP1	ENST00000561596.5	TSL:5	n.34-132473G>C		intron	N/A
	DISC1FP1	ENST00000562245.6	TSL:3	n.87-132473G>C		intron	N/A
	DISC1FP1	ENST00000649150.1		n.178+52659G>C		intron	N/A

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

African (AFR) AF: 0.647 AC: 26562 AN: 41056

American (AMR) AF: 0.712 AC: 10754 AN: 15100

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2074 AN: 3456

East Asian (EAS) AF: 0.756 AC: 3808 AN: 5038

South Asian (SAS) AF: 0.782 AC: 3716 AN: 4754

European-Finnish (FIN) AF: 0.621 AC: 6430 AN: 10352

Middle Eastern (MID) AF: 0.646 AC: 186 AN: 288

European-Non Finnish (NFE) AF: 0.624 AC: 42193 AN: 67584

Other (OTH) AF: 0.651 AC: 1364 AN: 2094

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.25
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs500737; hg19: chr11-90147449;