rs660753

Variant names:

• chr11-90639135-G-A
• rs660753
• ENST00000561596.5:n.279+36227G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-90639135-G-A
• chr11-90639135-G-T

Variant summary

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

The ENST00000562245.6(DISC1FP1):​n.332+36227G>A variant causes a intron 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 ENST00000562245.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562245.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DISC1FP1	NR_104190.1		n.332+36227G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DISC1FP1	ENST00000561596.5	TSL:5	n.279+36227G>A		intron	N/A
	DISC1FP1	ENST00000562245.6	TSL:3	n.332+36227G>A		intron	N/A
	DISC1FP1	ENST00000562678.5	TSL:3	n.185+92240G>A		intron	N/A

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

African (AFR) AF: 0.327 AC: 13528 AN: 41424

American (AMR) AF: 0.494 AC: 7544 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1922 AN: 3466

East Asian (EAS) AF: 0.542 AC: 2794 AN: 5158

South Asian (SAS) AF: 0.671 AC: 3231 AN: 4818

European-Finnish (FIN) AF: 0.449 AC: 4744 AN: 10554

Middle Eastern (MID) AF: 0.610 AC: 178 AN: 292

European-Non Finnish (NFE) AF: 0.552 AC: 37471 AN: 67932

Other (OTH) AF: 0.501 AC: 1055 AN: 2104

Alfa AF: 0.531 Hom.: 16833

Bravo AF: 0.470

Asia WGS AF: 0.620 AC: 2154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.95
DANN	Benign	0.16
PhyloP100		0.18

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs660753;

hg19: chr11-90372303;