rs7957346

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr12-95866696-C-A
• chr12-95866696-C-G
• chr12-95866696-C-T

Variant summary

Our verdict is Benign. The variant received -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
• 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: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000552085.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNRPF	ENST00000552085.1	TSL:3	c.129+5403C>A		intron	N/A	ENSP00000447127.1	F8W0W6
	SNRPF	ENST00000553192.5	TSL:4	c.129+5403C>A		intron	N/A	ENSP00000447751.1	A0A0B4J254
	SNRPF	ENST00000929920.1		c.*625C>A		downstream_gene	N/A	ENSP00000599979.1

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

African (AFR) AF: 0.618 AC: 147 AN: 238

American (AMR) AF: 0.443 AC: 108 AN: 244

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 118 AN: 254

East Asian (EAS) AF: 0.346 AC: 101 AN: 292

South Asian (SAS) AF: 0.578 AC: 118 AN: 204

European-Finnish (FIN) AF: 0.596 AC: 180 AN: 302

Middle Eastern (MID) AF: 0.368 AC: 14 AN: 38

European-Non Finnish (NFE) AF: 0.553 AC: 3105 AN: 5618

Other (OTH) AF: 0.506 AC: 247 AN: 488

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

African (AFR) AF: 0.626 AC: 25946 AN: 41456

American (AMR) AF: 0.479 AC: 7320 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1647 AN: 3470

East Asian (EAS) AF: 0.375 AC: 1940 AN: 5174

South Asian (SAS) AF: 0.595 AC: 2869 AN: 4818

European-Finnish (FIN) AF: 0.618 AC: 6522 AN: 10552

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 38957 AN: 67928

Other (OTH) AF: 0.541 AC: 1141 AN: 2110

Alfa AF: 0.576 Hom.: 10039

Bravo AF: 0.564

Asia WGS AF: 0.476 AC: 1655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.40
PhyloP100		0.030
Mutation Taster		=100/0	polymorphism (auto)

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;