rs333113

Variant names:

• chr17-4497061-C-G
• rs333113
• ENST00000416958.2:n.942G>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000416958.2(SPNS2-AS1):​n.942G>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 ENST00000416958.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659
• Publications: 6 publications found

Genes affected

SPNS2-AS1 (HGNC:55787): (SPNS2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416958.2. 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
	SPNS2-AS1	ENST00000416958.2	TSL:3	n.942G>C		non_coding_transcript_exon	Exon 2 of 2
	SPNS2-AS1	ENST00000809720.1		n.427+481G>C		intron	N/A
	SPNS2-AS1	ENST00000809721.1		n.427+481G>C		intron	N/A

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

African (AFR) AF: 0.857 AC: 35621 AN: 41548

American (AMR) AF: 0.577 AC: 8827 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2849 AN: 3466

East Asian (EAS) AF: 0.0147 AC: 76 AN: 5170

South Asian (SAS) AF: 0.547 AC: 2641 AN: 4824

European-Finnish (FIN) AF: 0.690 AC: 7305 AN: 10588

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53472 AN: 68004

Other (OTH) AF: 0.738 AC: 1560 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.35
DANN	Benign	0.41
PhyloP100		-0.66

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs333113;

hg19: chr17-4400356;

COSMIC: COSV61231578;