rs1634481

Positions:

• chr17-36078317-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000620056.4(CCL3-AS1):​n.389+2942A>G variant causes a intron, non coding transcript 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 ENST00000620056.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCL3-AS1	ENST00000620056.4	n.389+2942A>G		intron_variant, non_coding_transcript_variant		5
CCL3-AS1	ENST00000610845.1	n.393+1515A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.0553

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.205

Alfa AF: 0.219 Hom.: 695

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1634481; hg19: chr17-34405675;