chr3-107420463-G-C

Variant names:

• chr3-107420463-G-C
• rs17808412
• ENST00000595232.2:n.110+732C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000595232.2(CCDC54-AS1):​n.110+732C>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.616
• Publications: 1 publications found

Genes affected

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

DUBR (HGNC:48569): (DPPA2 upstream binding RNA) Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II; positive regulation of myoblast differentiation; and regulation of DNA methylation. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

LINC01990 (HGNC:52822): (long intergenic non-protein coding RNA 1990)

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 157 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC54-AS1	ENST00000595232.2	n.110+732C>G		intron_variant	Intron 1 of 3	5
CCDC54-AS1	ENST00000599431.3	n.27+732C>G		intron_variant	Intron 1 of 4	5
CCDC54-AS1	ENST00000658011.1	n.144+732C>G		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.00896 AC: 372 AN: 41540

American (AMR) AF: 0.0329 AC: 503 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0597 AC: 207 AN: 3468

East Asian (EAS) AF: 0.0166 AC: 86 AN: 5184

South Asian (SAS) AF: 0.0399 AC: 192 AN: 4818

European-Finnish (FIN) AF: 0.0919 AC: 973 AN: 10584

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0492 AC: 3348 AN: 68006

Other (OTH) AF: 0.0464 AC: 98 AN: 2112

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
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs17808412; hg19: chr3-107139310;