rs10501718

chr11-90289118-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.86+37801G>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 0.0516 in 152,158 control chromosomes in the GnomAD database, including 478 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 0.052 (478 hom., cov: 32)
• Consequence: DISC1FP1 NR_104190.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.868

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=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DISC1FP1	NR_104190.1	n.86+37801G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DISC1FP1	ENST00000649150.1	n.114+37801G>C		intron_variant, non_coding_transcript_variant
DISC1FP1	ENST00000561596.5	n.33+37801G>C		intron_variant, non_coding_transcript_variant		5
DISC1FP1	ENST00000562245.5	n.86+37801G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0516 AC: 7838 AN: 152038 Hom.: 477 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0226

Gnomad ASJ AF: 0.0418

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00290

Gnomad FIN AF: 0.00501

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0164

Gnomad OTH AF: 0.0393

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

GnomAD4 genome AF: 0.0516 AC: 7852 AN: 152158 Hom.: 478 Cov.: 32 AF XY: 0.0487 AC XY: 3624 AN XY: 74392

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.0226

Gnomad4 ASJ AF: 0.0418

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00290

Gnomad4 FIN AF: 0.00501

Gnomad4 NFE AF: 0.0164

Gnomad4 OTH AF: 0.0389

Alfa AF: 0.0394 Hom.: 39

Bravo AF: 0.0579

Asia WGS AF: 0.00982 AC: 35 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
Cadd	Benign	19
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501718; hg19: chr11-90022286;