chr17-4497061-C-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000416958.2(SPNS2-AS1):​n.942G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPNS2-AS1	XR_001752762.1	n.1221G>A		non_coding_transcript_exon_variant	Exon 2 of 3
SPNS2-AS1	XR_007065584.1	n.984G>A		non_coding_transcript_exon_variant	Exon 3 of 3
SPNS2-AS1	XR_001752763.2	n.759+481G>A		intron_variant	Intron 2 of 2
SPNS2-AS1	XR_001752764.1	n.1110+111G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPNS2-AS1	ENST00000416958.2	n.942G>A		non_coding_transcript_exon_variant	Exon 2 of 2	3
SPNS2-AS1	ENST00000809720.1	n.427+481G>A		intron_variant	Intron 2 of 3
SPNS2-AS1	ENST00000809721.1	n.427+481G>A		intron_variant	Intron 2 of 2
SPNS2-AS1	ENST00000809722.1	n.541+481G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 2371

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.45
DANN	Benign	0.90
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs333113; hg19: chr17-4400356;