chr12-95866696-C-A

Variant names:

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

Variant summary

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

The ENST00000552085.1(SNRPF):​c.129+5403C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 159,660 control chromosomes in the GnomAD database, including 26,402 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 0.57 (25248 hom., cov: 33)
  • Exomes 𝑓: 0.54 (1154 hom.)
• Consequence: SNRPF ENST00000552085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

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>A		intron_variant	Intron 2 of 4	3		ENSP00000447127.1
SNRPF	ENST00000553192.5	c.129+5403C>A		intron_variant	Intron 2 of 2	4		ENSP00000447751.1
SNRPF	ENST00000549580.1	n.*245C>A		downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86908 AN: 151864 Hom.: 25233 Cov.: 33

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.545

GnomAD4 exome AF: 0.539 AC: 4138 AN: 7678 Hom.: 1154 Cov.: 0 AF XY: 0.541 AC XY: 2145 AN XY: 3962

Gnomad4 AFR exome AF: 0.618

Gnomad4 AMR exome AF: 0.443

Gnomad4 ASJ exome AF: 0.465

Gnomad4 EAS exome AF: 0.346

Gnomad4 SAS exome AF: 0.578

Gnomad4 FIN exome AF: 0.596

Gnomad4 NFE exome AF: 0.553

Gnomad4 OTH exome AF: 0.506

GnomAD4 genome AF: 0.572 AC: 86965 AN: 151982 Hom.: 25248 Cov.: 33 AF XY: 0.572 AC XY: 42518 AN XY: 74294

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.541

Alfa AF: 0.587 Hom.: 5438

Bravo AF: 0.564

Asia WGS AF: 0.476 AC: 1655 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	1.5
DANN	Benign	0.40

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: rs7957346; hg19: chr12-96260474;