11-90853732-C-T

Variant names:

• chr11-90853732-C-T
• rs12274302
• ENST00000569513.1:n.1668C>T

Variant summary

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

The ENST00000569513.1(DISC1FP1):​n.1668C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0514 in 149,706 control chromosomes in the GnomAD database, including 659 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 0.051 (659 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: DISC1FP1 ENST00000569513.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000569513.1. 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.591+1025C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DISC1FP1	ENST00000569513.1	TSL:6	n.1668C>T		non_coding_transcript_exon	Exon 1 of 1
	DISC1FP1	ENST00000561596.5	TSL:5	n.538+1025C>T		intron	N/A
	DISC1FP1	ENST00000562245.6	TSL:3	n.591+1025C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0512 AC: 7660 AN: 149592 Hom.: 654 Cov.: 31

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0235

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000210

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000800

Gnomad OTH AF: 0.0423

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 18 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 12

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 8

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.0514 AC: 7696 AN: 149706 Hom.: 659 Cov.: 31 AF XY: 0.0492 AC XY: 3587 AN XY: 72876

African (AFR) AF: 0.177 AC: 7194 AN: 40744

American (AMR) AF: 0.0235 AC: 350 AN: 14910

Ashkenazi Jewish (ASJ) AF: 0.00202 AC: 7 AN: 3458

East Asian (EAS) AF: 0.00 AC: 0 AN: 5044

South Asian (SAS) AF: 0.000211 AC: 1 AN: 4748

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10076

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.000801 AC: 54 AN: 67450

Other (OTH) AF: 0.0418 AC: 87 AN: 2080

Alfa AF: 0.0198 Hom.: 519

Bravo AF: 0.0594

Asia WGS AF: 0.0170 AC: 61 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.70
PhyloP100		-0.14

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: rs12274302;

hg19: chr11-90586900;