chr12-95866696-C-T

Variant names:

• chr12-95866696-C-T
• rs7957346
• ENST00000552085.1:c.129+5403C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000552085.1(SNRPF):​c.129+5403C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SNRPF ENST00000552085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 5 publications found

Genes affected

SNRPF (HGNC:11162): (small nuclear ribonucleoprotein polypeptide F) Enables RNA binding activity. Involved in spliceosomal snRNP assembly. Located in cytosol and nucleus. Part of several cellular components, including methylosome; nucleus; and pICln-Sm protein complex. Biomarker of nasopharynx carcinoma. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNRPF	ENST00000552085.1	c.129+5403C>T		intron_variant	Intron 2 of 4	3		ENSP00000447127.1
SNRPF	ENST00000553192.5	c.129+5403C>T		intron_variant	Intron 2 of 2	4		ENSP00000447751.1
SNRPF	ENST00000549580.1	n.*245C>T		downstream_gene_variant		2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 7706 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 3970

African (AFR) AF: 0.00 AC: 0 AN: 238

American (AMR) AF: 0.00 AC: 0 AN: 244

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 258

East Asian (EAS) AF: 0.00 AC: 0 AN: 294

South Asian (SAS) AF: 0.00 AC: 0 AN: 204

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 304

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 38

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 5638

Other (OTH) AF: 0.00 AC: 0 AN: 488

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.9
DANN	Benign	0.93
PhyloP100		0.030

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

Other links and lift over

dbSNP: rs7957346; hg19: chr12-96260474;