rs9895785

Positions:

• chr17-30780690-T-C

Variant summary

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

The NR_144395.1(SUZ12P1):​n.846-4093T>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 0.127 in 152,048 control chromosomes in the GnomAD database, including 1,282 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 0.13 (1282 hom., cov: 31)
• Consequence: SUZ12P1 NR_144395.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

SUZ12P1 (HGNC:):

CRLF3 (HGNC:17177): (cytokine receptor like factor 3) This gene encodes a cytokine receptor-like factor that may negatively regulate cell cycle progression at the G0/G1 phase. Studies of the related rat protein suggest that it may regulate neuronal morphology and synaptic vesicle biogenesis. This gene is one of several genes located in the neurofibromatosis type I tumor suppressor region on the q arm of chromosome 17, a region that is subject to microdeletions, duplications, chromosomal breaks and rearrangements. Alternative splicing of this gene results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 2 and 5. [provided by RefSeq, Aug 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUZ12P1	NR_144395.1	n.846-4093T>C		intron_variant, non_coding_transcript_variant
SUZ12P1	NR_144394.1	n.734-4093T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRLF3	ENST00000583527.1	c.212+3617A>G		intron_variant		5		ENSP00000463689
	ENST00000582329.1	n.412-6037T>C		intron_variant, non_coding_transcript_variant		5
CRLF3	ENST00000585268.1	n.107+3617A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19248 AN: 151930 Hom.: 1278 Cov.: 31

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.0851

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.127 AC: 19278 AN: 152048 Hom.: 1282 Cov.: 31 AF XY: 0.128 AC XY: 9481 AN XY: 74330

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.0851

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.123

Alfa AF: 0.121 Hom.: 1755

Bravo AF: 0.132

Asia WGS AF: 0.198 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9895785; hg19: chr17-29107708;