chr6-138755633-T-C

Variant names:

• chr6-138755633-T-C
• rs4321841
• ENST00000615663.2:n.430+384A>G

Variant summary

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

The ENST00000615663.2(CCDC28A-AS1):​n.430+384A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 152,000 control chromosomes in the GnomAD database, including 29,829 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 0.61 (29829 hom., cov: 32)
• Consequence: CCDC28A-AS1 ENST00000615663.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67
• Publications: 8 publications found

Genes affected

CCDC28A-AS1 (HGNC:51715): (CCDC28A antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000615663.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC28A-AS1	NR_161203.1		n.312-5364A>G		intron	N/A
	CCDC28A-AS1	NR_161204.1		n.619+8624A>G		intron	N/A
	CCDC28A-AS1	NR_161205.1		n.311+8624A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC28A-AS1	ENST00000615663.2	TSL:3	n.430+384A>G		intron	N/A
	CCDC28A-AS1	ENST00000624173.1	TSL:2	n.261-5364A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92209 AN: 151882 Hom.: 29799 Cov.: 32

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.607 AC: 92296 AN: 152000 Hom.: 29829 Cov.: 32 AF XY: 0.610 AC XY: 45314 AN XY: 74304

African (AFR) AF: 0.793 AC: 32888 AN: 41462

American (AMR) AF: 0.655 AC: 9987 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1993 AN: 3472

East Asian (EAS) AF: 0.891 AC: 4619 AN: 5184

South Asian (SAS) AF: 0.745 AC: 3593 AN: 4820

European-Finnish (FIN) AF: 0.459 AC: 4847 AN: 10552

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.477 AC: 32390 AN: 67946

Other (OTH) AF: 0.623 AC: 1310 AN: 2104

Alfa AF: 0.522 Hom.: 16898

Bravo AF: 0.629

Asia WGS AF: 0.797 AC: 2765 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.3
DANN	Benign	0.75
PhyloP100		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4321841; hg19: chr6-139076770;