rs4321841

chr6-138755633-T-Cchr6-138755633-T-G

Variant summary

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

The NR_161205.1(CCDC28A-AS1):n.311+8624A>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 0.607 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 NR_161205.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC28A-AS1	NR_161205.1	n.311+8624A>G		intron_variant, non_coding_transcript_variant
CCDC28A-AS1	NR_161203.1	n.312-5364A>G		intron_variant, non_coding_transcript_variant
CCDC28A-AS1	NR_161204.1	n.619+8624A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC28A-AS1	ENST00000624173.1	n.261-5364A>G		intron_variant, non_coding_transcript_variant		2
CCDC28A-AS1	ENST00000615663.2	n.430+384A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.745

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.623

Alfa AF: 0.523 Hom.: 12899

Bravo AF: 0.629

Asia WGS AF: 0.797 AC: 2765 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	9.3
Dann	Benign	0.75

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

Publications

LitVar

Other links and lift over

dbSNP: rs4321841; hg19: chr6-139076770;