12-26300350-A-G

Variant names:

• chr12-26300350-A-G
• rs718314
• ENST00000540392.1:n.130+26034T>C

Variant summary

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

The ENST00000540392.1(SSPN-AS1):​n.130+26034T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,918 control chromosomes in the GnomAD database, including 6,805 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 0.28 (6805 hom., cov: 32)
• Consequence: SSPN-AS1 ENST00000540392.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489
• Publications: 110 publications found

Genes affected

SSPN-AS1 (HGNC:56072): (ITPR2 and SSPN antisense RNA 1)

ENSG00000255750 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000540392.1. 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
	SSPN-AS1	ENST00000540392.1	TSL:3	n.130+26034T>C		intron	N/A
	ENSG00000255750	ENST00000540625.5	TSL:3	n.119+19252T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41797 AN: 151800 Hom.: 6796 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.275 AC: 41834 AN: 151918 Hom.: 6805 Cov.: 32 AF XY: 0.281 AC XY: 20856 AN XY: 74240

African (AFR) AF: 0.201 AC: 8304 AN: 41406

American (AMR) AF: 0.455 AC: 6954 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 819 AN: 3464

East Asian (EAS) AF: 0.697 AC: 3605 AN: 5174

South Asian (SAS) AF: 0.243 AC: 1171 AN: 4814

European-Finnish (FIN) AF: 0.294 AC: 3094 AN: 10524

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17051 AN: 67948

Other (OTH) AF: 0.285 AC: 601 AN: 2110

Alfa AF: 0.269 Hom.: 28806

Bravo AF: 0.287

Asia WGS AF: 0.412 AC: 1432 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.15
DANN	Benign	0.31
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs718314; hg19: chr12-26453283;