3-107360387-A-G

Variant summary

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

The ENST00000595232.2(CCDC54-AS1):n.488+20198T>C 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 0.939 in 152,134 control chromosomes in the GnomAD database, including 67,409 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 0.94 (67409 hom., cov: 30)
• Consequence: CCDC54-AS1 ENST00000595232.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22

Genes affected

CCDC54-AS1 (HGNC:56107): (CCDC54 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC54-AS1	ENST00000595232.2	n.488+20198T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.939 AC: 142686 AN: 152016 Hom.: 67353 Cov.: 30

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.970

Gnomad ASJ AF: 0.960

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.940

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

GnomAD4 genome AF: 0.939 AC: 142801 AN: 152134 Hom.: 67409 Cov.: 30 AF XY: 0.941 AC XY: 69977 AN XY: 74380

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.970

Gnomad4 ASJ AF: 0.960

Gnomad4 EAS AF: 0.945

Gnomad4 SAS AF: 0.961

Gnomad4 FIN AF: 0.997

Gnomad4 NFE AF: 0.986

Gnomad4 OTH AF: 0.940

Alfa AF: 0.976 Hom.: 3432

Bravo AF: 0.931

Asia WGS AF: 0.949 AC: 3298 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.27
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs709552; hg19: chr3-107079234;