rs17808412

chr3-107420463-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000595232.2(CCDC54-AS1):n.110+732C>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 0.0386 in 152,202 control chromosomes in the GnomAD database, including 157 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 0.039 (157 hom., cov: 32)
• Consequence: CCDC54-AS1 ENST00000595232.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.616

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=-0.83).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0386 (5876/152202) while in subpopulation NFE AF= 0.0492 (3348/68006). AF 95% confidence interval is 0.0478. There are 157 homozygotes in gnomad4. There are 3003 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 157 gene

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.110+732C>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0386 AC: 5877 AN: 152084 Hom.: 157 Cov.: 32

Gnomad AFR AF: 0.00898

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0330

Gnomad ASJ AF: 0.0597

Gnomad EAS AF: 0.0166

Gnomad SAS AF: 0.0398

Gnomad FIN AF: 0.0919

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0492

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0386 AC: 5876 AN: 152202 Hom.: 157 Cov.: 32 AF XY: 0.0404 AC XY: 3003 AN XY: 74398

Gnomad4 AFR AF: 0.00896

Gnomad4 AMR AF: 0.0329

Gnomad4 ASJ AF: 0.0597

Gnomad4 EAS AF: 0.0166

Gnomad4 SAS AF: 0.0399

Gnomad4 FIN AF: 0.0919

Gnomad4 NFE AF: 0.0492

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0464 Hom.: 17

Bravo AF: 0.0332

Asia WGS AF: 0.0210 AC: 73 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	6.4
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17808412; hg19: chr3-107139310;