rs333113

Positions:

• chr17-4497061-C-G
• chr17-4497061-C-T

Variant summary

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

The XR_001752762.1(SPNS2-AS1):​n.1221G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 152,218 control chromosomes in the GnomAD database, including 44,472 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 0.74 (44472 hom., cov: 33)
• Consequence: SPNS2-AS1 XR_001752762.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659

Genes affected

SPNS2-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPNS2-AS1	XR_001752762.1	n.1221G>C		non_coding_transcript_exon_variant	2/3
SPNS2-AS1	XR_007065584.1	n.984G>C		non_coding_transcript_exon_variant	3/3
		n.4497061C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.744 AC: 113210 AN: 152100 Hom.: 44443 Cov.: 33

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.0147

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.744 AC: 113283 AN: 152218 Hom.: 44472 Cov.: 33 AF XY: 0.729 AC XY: 54225 AN XY: 74404

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.822

Gnomad4 EAS AF: 0.0147

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.786

Gnomad4 OTH AF: 0.738

Alfa AF: 0.696 Hom.: 2371

Bravo AF: 0.739

Asia WGS AF: 0.281 AC: 983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.35
DANN	Benign	0.41

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs333113; hg19: chr17-4400356; COSMIC: COSV61231578;