7-28974579-G-T

Variant names:

• chr7-28974579-G-T
• rs2018683
• ENST00000749297.1:n.295+15530G>T

Variant summary

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

The ENST00000749297.1(CPVL-AS2):​n.295+15530G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 149,076 control chromosomes in the GnomAD database, including 17,918 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 0.47 (17918 hom., cov: 27)
• Consequence: CPVL-AS2 ENST00000749297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100
• Publications: 15 publications found

Genes affected

CPVL-AS2 (HGNC:56138): (CPVL antisense RNA 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000749297.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPVL-AS2	ENST00000749297.1		n.295+15530G>T		intron	N/A
	CPVL-AS2	ENST00000749298.1		n.474+15530G>T		intron	N/A
	CPVL-AS2	ENST00000749299.1		n.198+15530G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.469 AC: 69869 AN: 148980 Hom.: 17913 Cov.: 27

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.469 AC: 69892 AN: 149076 Hom.: 17918 Cov.: 27 AF XY: 0.461 AC XY: 33363 AN XY: 72384

African (AFR) AF: 0.272 AC: 10991 AN: 40478

American (AMR) AF: 0.502 AC: 7528 AN: 14982

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1714 AN: 3444

East Asian (EAS) AF: 0.269 AC: 1328 AN: 4946

South Asian (SAS) AF: 0.508 AC: 2404 AN: 4736

European-Finnish (FIN) AF: 0.468 AC: 4452 AN: 9506

Middle Eastern (MID) AF: 0.475 AC: 135 AN: 284

European-Non Finnish (NFE) AF: 0.590 AC: 39981 AN: 67720

Other (OTH) AF: 0.505 AC: 1047 AN: 2074

Alfa AF: 0.522 Hom.: 35371

Bravo AF: 0.462

Asia WGS AF: 0.358 AC: 1244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	0.84
DANN	Benign	0.85
PhyloP100		-0.0010

Splicing

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

Other links and lift over

dbSNP: rs2018683; hg19: chr7-29014195;