rs854477

Variant names:

• chr17-36075798-A-G
• rs854477
• ENST00000610845.1:n.301-912A>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.301-912A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 152,132 control chromosomes in the GnomAD database, including 46,410 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 0.77 (46410 hom., cov: 32)
• Consequence: CCL3-AS1 ENST00000610845.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCL3-AS1	NR_186417.1	n.237-912A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCL3-AS1	ENST00000610845.1	n.301-912A>G		intron_variant	Intron 3 of 4	5
CCL3-AS1	ENST00000615750.2	n.237-912A>G		intron_variant	Intron 1 of 3	3
CCL3-AS1	ENST00000620056.4	n.389+423A>G		intron_variant	Intron 3 of 3	5
CCL3-AS1	ENST00000818634.1	n.242-912A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117479 AN: 152014 Hom.: 46339 Cov.: 32

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.773 AC: 117614 AN: 152132 Hom.: 46410 Cov.: 32 AF XY: 0.776 AC XY: 57688 AN XY: 74380

African (AFR) AF: 0.938 AC: 38938 AN: 41526

American (AMR) AF: 0.779 AC: 11896 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2729 AN: 3468

East Asian (EAS) AF: 0.675 AC: 3486 AN: 5164

South Asian (SAS) AF: 0.775 AC: 3737 AN: 4820

European-Finnish (FIN) AF: 0.733 AC: 7753 AN: 10576

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46596 AN: 67992

Other (OTH) AF: 0.776 AC: 1638 AN: 2110

Alfa AF: 0.721 Hom.: 129122

Bravo AF: 0.782

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs854477; hg19: chr17-34403158;