17-36076917-C-T

Variant names:

• chr17-36076917-C-T
• rs1719220
• ENST00000610845.1:n.393+115C>T

Variant summary

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

The ENST00000615750.2(CCL3-AS1):​n.329+115C>T 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 152,116 control chromosomes in the GnomAD database, including 3,763 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 (3763 hom., cov: 31)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: CCL3-AS1 ENST00000615750.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 7 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=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000615750.2. 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
	CCL3-AS1	NR_186417.1		n.329+115C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCL3-AS1	ENST00000610845.1	TSL:5	n.393+115C>T		intron	N/A
	CCL3-AS1	ENST00000615750.2	TSL:3	n.329+115C>T		intron	N/A
	CCL3-AS1	ENST00000620056.4	TSL:5	n.389+1542C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30450 AN: 151992 Hom.: 3767 Cov.: 31

Gnomad AFR AF: 0.0552

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.210

GnomAD4 exome AF: 0.167 AC: 1 AN: 6 Hom.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.200 AC: 30437 AN: 152110 Hom.: 3763 Cov.: 31 AF XY: 0.198 AC XY: 14708 AN XY: 74352

African (AFR) AF: 0.0552 AC: 2291 AN: 41514

American (AMR) AF: 0.206 AC: 3148 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 699 AN: 3470

East Asian (EAS) AF: 0.327 AC: 1693 AN: 5172

South Asian (SAS) AF: 0.226 AC: 1089 AN: 4824

European-Finnish (FIN) AF: 0.208 AC: 2202 AN: 10568

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.273 AC: 18521 AN: 67962

Other (OTH) AF: 0.207 AC: 436 AN: 2108

Alfa AF: 0.250 Hom.: 3694

Bravo AF: 0.195

Asia WGS AF: 0.275 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	7.2
DANN	Benign	0.67
PhyloP100		0.22

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1719220;

hg19: chr17-34404277;