rs10830528

Positions:

• chr11-90536652-T-C

Variant summary

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

The NR_104190.1(DISC1FP1):​n.87-10102T>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 0.207 in 152,050 control chromosomes in the GnomAD database, including 3,772 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 0.21 (3772 hom., cov: 32)
• Consequence: DISC1FP1 NR_104190.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DISC1FP1	NR_104190.1	n.87-10102T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DISC1FP1	ENST00000649150.1	n.179-10102T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31467 AN: 151932 Hom.: 3754 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.207 AC: 31520 AN: 152050 Hom.: 3772 Cov.: 32 AF XY: 0.212 AC XY: 15739 AN XY: 74314

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.205

Alfa AF: 0.175 Hom.: 328

Bravo AF: 0.220

Asia WGS AF: 0.282 AC: 981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10830528; hg19: chr11-90269820;