ENST00000610845.1:n.393+1515A>G

Variant names:

• chr17-36078317-A-G
• rs1634481
• ENST00000610845.1:n.393+1515A>G

Variant summary

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

The ENST00000610845.1(CCL3-AS1):​n.393+1515A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,130 control chromosomes in the GnomAD database, including 3,758 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 0.20 (3758 hom., cov: 32)
• Consequence: CCL3-AS1 ENST00000610845.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• Publications: 2 publications found

Genes affected

CCL3-AS1 (HGNC:55229): (CCL3 antisense RNA 1)

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 = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCL3-AS1	NR_186417.1	n.329+1515A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCL3-AS1	ENST00000610845.1	n.393+1515A>G		intron_variant	Intron 4 of 4	5
CCL3-AS1	ENST00000615750.2	n.329+1515A>G		intron_variant	Intron 2 of 3	3
CCL3-AS1	ENST00000620056.4	n.389+2942A>G		intron_variant	Intron 3 of 3	5
CCL3-AS1	ENST00000818634.1	n.334+1515A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30448 AN: 152012 Hom.: 3762 Cov.: 32

Gnomad AFR AF: 0.0553

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.200 AC: 30435 AN: 152130 Hom.: 3758 Cov.: 32 AF XY: 0.198 AC XY: 14696 AN XY: 74364

African (AFR) AF: 0.0553 AC: 2295 AN: 41530

American (AMR) AF: 0.206 AC: 3147 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 700 AN: 3466

East Asian (EAS) AF: 0.328 AC: 1692 AN: 5166

South Asian (SAS) AF: 0.226 AC: 1091 AN: 4828

European-Finnish (FIN) AF: 0.208 AC: 2201 AN: 10584

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18521 AN: 67964

Other (OTH) AF: 0.205 AC: 430 AN: 2102

Alfa AF: 0.235 Hom.: 1525

Bravo AF: 0.195

Asia WGS AF: 0.275 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.70
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1634481; hg19: chr17-34405675;