rs7957346

chr12-95866696-C-Achr12-95866696-C-Gchr12-95866696-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNRPF	ENST00000552085.1	c.129+5403C>A		intron_variant		3
SNRPF	ENST00000553192.5	c.129+5403C>A		intron_variant		4

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;