rs4762633

Positions:

• chr12-95860295-C-T

Variant summary

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

The NM_003095.5(SNRPF):​c.4-873C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,158 control chromosomes in the GnomAD database, including 50,526 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 0.81 (50526 hom., cov: 32)
• Consequence: SNRPF NM_003095.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNRPF	NM_003095.5	c.4-873C>T		intron_variant		ENST00000266735.10	NP_003086.1
SNRPF	NM_001394209.1	c.4-873C>T		intron_variant			NP_001381138.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNRPF	ENST00000266735.10	c.4-873C>T		intron_variant		1	NM_003095.5	ENSP00000266735	P1
SNRPF	ENST00000552085.1	c.4-873C>T		intron_variant		3		ENSP00000447127
SNRPF	ENST00000553192.5	c.4-873C>T		intron_variant		4		ENSP00000447751
SNRPF	ENST00000551316.1	n.114-873C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123253 AN: 152040 Hom.: 50485 Cov.: 32

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.900

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.811 AC: 123344 AN: 152158 Hom.: 50526 Cov.: 32 AF XY: 0.812 AC XY: 60372 AN XY: 74382

Gnomad4 AFR AF: 0.880

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.760

Gnomad4 SAS AF: 0.799

Gnomad4 FIN AF: 0.900

Gnomad4 NFE AF: 0.805

Gnomad4 OTH AF: 0.791

Alfa AF: 0.817 Hom.: 6346

Bravo AF: 0.792

Asia WGS AF: 0.795 AC: 2764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.4
DANN	Benign	0.24

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: rs4762633; hg19: chr12-96254073;