rs9895785

Variant names:

• chr17-30780690-T-C
• rs9895785
• ENST00000583527.1:c.210+3617A>G

Variant summary

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

The ENST00000583527.1(CRLF3):​c.210+3617A>G variant causes a intron 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: CRLF3 ENST00000583527.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 19 publications found

Genes affected

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]

ENSG00000290928 (HGNC:):

SUZ12P1 (HGNC:32421): (SUZ12 pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SUZ12P1	NR_144394.1	n.734-4093T>C		intron_variant	Intron 6 of 8
SUZ12P1	NR_144395.1	n.846-4093T>C		intron_variant	Intron 8 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRLF3	ENST00000583527.1	c.210+3617A>G		intron_variant	Intron 2 of 3	5		ENSP00000463689.1
ENSG00000290928	ENST00000582329.1	n.412-6037T>C		intron_variant	Intron 3 of 4	5
CRLF3	ENST00000585268.1	n.107+3617A>G		intron_variant	Intron 1 of 3	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

African (AFR) AF: 0.137 AC: 5679 AN: 41476

American (AMR) AF: 0.159 AC: 2427 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 354 AN: 3466

East Asian (EAS) AF: 0.132 AC: 681 AN: 5178

South Asian (SAS) AF: 0.248 AC: 1196 AN: 4818

European-Finnish (FIN) AF: 0.0851 AC: 901 AN: 10592

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7594 AN: 67984

Other (OTH) AF: 0.123 AC: 259 AN: 2098

Alfa AF: 0.121 Hom.: 2413

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9895785; hg19: chr17-29107708;