3-150979421-C-T

Variant names:

• chr3-150979421-C-T
• rs16863118
• ENST00000465576.1:n.416+6328C>T

Variant summary

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

The ENST00000465576.1(SIAH2-AS1):​n.416+6328C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,130 control chromosomes in the GnomAD database, including 2,798 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 0.18 (2798 hom., cov: 32)
• Consequence: SIAH2-AS1 ENST00000465576.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 4 publications found

Genes affected

SIAH2-AS1 (HGNC:40526): (SIAH2 antisense RNA 1)

ENSG00000243273 (HGNC:):

CLRN1-AS1 (HGNC:30895): (CLRN1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLRN1-AS1	NR_024066.2	n.416+6328C>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SIAH2-AS1	ENST00000465576.1	n.416+6328C>T		intron_variant	Intron 1 of 5	1
ENSG00000243273	ENST00000469268.1	n.236-22153C>T		intron_variant	Intron 1 of 2	4
SIAH2-AS1	ENST00000476886.5	n.124-83505C>T		intron_variant	Intron 1 of 4	2
SIAH2-AS1	ENST00000716210.1	n.447-74441C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27599 AN: 152012 Hom.: 2787 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.182 AC: 27638 AN: 152130 Hom.: 2798 Cov.: 32 AF XY: 0.188 AC XY: 13991 AN XY: 74366

African (AFR) AF: 0.218 AC: 9061 AN: 41516

American (AMR) AF: 0.219 AC: 3347 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 424 AN: 3470

East Asian (EAS) AF: 0.387 AC: 2002 AN: 5176

South Asian (SAS) AF: 0.140 AC: 675 AN: 4822

European-Finnish (FIN) AF: 0.216 AC: 2286 AN: 10566

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9269 AN: 67986

Other (OTH) AF: 0.186 AC: 393 AN: 2110

Alfa AF: 0.152 Hom.: 6280

Bravo AF: 0.186

Asia WGS AF: 0.261 AC: 904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.099
DANN	Benign	0.20
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs16863118; hg19: chr3-150697208;