rs12523164

Variant names:

• chr5-127726279-T-C
• rs12523164
• NM_001317938.2:c.114+18519T>C

Variant summary

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

The NM_001317938.2(CCDC192):​c.114+18519T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0558 in 152,306 control chromosomes in the GnomAD database, including 553 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 0.056 (553 hom., cov: 33)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490
• Publications: 3 publications found

Genes affected

CCDC192 (HGNC:49566): (coiled-coil domain containing 192)

ENSG00000248799 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC192	NM_001317938.2	c.114+18519T>C		intron_variant	Intron 2 of 6	ENST00000514853.5	NP_001304867.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC192	ENST00000514853.5	c.114+18519T>C		intron_variant	Intron 2 of 6	5	NM_001317938.2	ENSP00000490579.2
CCDC192	ENST00000706942.1	c.171+18519T>C		intron_variant	Intron 2 of 6			ENSP00000516662.1
ENSG00000248799	ENST00000827054.1	n.95-16880A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0557 AC: 8483 AN: 152188 Hom.: 552 Cov.: 33

Gnomad AFR AF: 0.0831

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0956

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.0862

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0107

Gnomad OTH AF: 0.0698

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

GnomAD4 genome AF: 0.0558 AC: 8493 AN: 152306 Hom.: 553 Cov.: 33 AF XY: 0.0588 AC XY: 4379 AN XY: 74466

African (AFR) AF: 0.0830 AC: 3450 AN: 41556

American (AMR) AF: 0.128 AC: 1959 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0956 AC: 332 AN: 3472

East Asian (EAS) AF: 0.271 AC: 1405 AN: 5186

South Asian (SAS) AF: 0.0864 AC: 417 AN: 4824

European-Finnish (FIN) AF: 0.00104 AC: 11 AN: 10622

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0107 AC: 728 AN: 68020

Other (OTH) AF: 0.0728 AC: 154 AN: 2114

Alfa AF: 0.0600 Hom.: 225

Bravo AF: 0.0677

Asia WGS AF: 0.175 AC: 608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.80
PhyloP100		0.049

Splicing

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

Other links and lift over

dbSNP: rs12523164; hg19: chr5-127061971;