rs1061346

chr17-30787211-G-Achr17-30787211-G-T

Variant summary

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

The NM_015986.4(CRLF3):c.960-1180C>T 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 152,184 control chromosomes in the GnomAD database, including 1,294 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 (1294 hom., cov: 32)
• Consequence: CRLF3 NM_015986.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.898

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]

SUZ12P1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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	UniProt
CRLF3	NM_015986.4	c.960-1180C>T		intron_variant		ENST00000324238.7
SUZ12P1	NR_144395.1	n.955+2319G>A		intron_variant, non_coding_transcript_variant
CRLF3	NR_073118.2	n.793-1180C>T		intron_variant, non_coding_transcript_variant
SUZ12P1	NR_144394.1	n.844-228G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRLF3	ENST00000324238.7	c.960-1180C>T		intron_variant		1	NM_015986.4	P1

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19312 AN: 152064 Hom.: 1290 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.0849

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.127 AC: 19342 AN: 152184 Hom.: 1294 Cov.: 32 AF XY: 0.128 AC XY: 9509 AN XY: 74408

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.0849

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.124

Alfa AF: 0.107 Hom.: 813

Bravo AF: 0.132

Asia WGS AF: 0.198 AC: 690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.3
Dann	Benign	0.52

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1061346; hg19: chr17-29114229;