NM_001317938.2:c.114+10826T>G

Variant names:

• chr5-127718586-T-G
• rs4835929
• NM_001317938.2:c.114+10826T>G

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+10826T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.058 in 152,236 control chromosomes in the GnomAD database, including 574 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 0.058 (574 hom., cov: 32)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.21
• Publications: 6 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC192	NM_001317938.2	c.114+10826T>G		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+10826T>G		intron_variant	Intron 2 of 6	5	NM_001317938.2	ENSP00000490579.2
CCDC192	ENST00000706942.1	c.171+10826T>G		intron_variant	Intron 2 of 6			ENSP00000516662.1
ENSG00000248799	ENST00000827054.1	n.95-9187A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0580 AC: 8824 AN: 152118 Hom.: 573 Cov.: 32

Gnomad AFR AF: 0.0918

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0954

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.0832

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.0107

Gnomad OTH AF: 0.0704

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

GnomAD4 genome AF: 0.0580 AC: 8835 AN: 152236 Hom.: 574 Cov.: 32 AF XY: 0.0609 AC XY: 4531 AN XY: 74444

African (AFR) AF: 0.0917 AC: 3808 AN: 41514

American (AMR) AF: 0.129 AC: 1966 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0954 AC: 331 AN: 3470

East Asian (EAS) AF: 0.269 AC: 1395 AN: 5182

South Asian (SAS) AF: 0.0835 AC: 403 AN: 4826

European-Finnish (FIN) AF: 0.00104 AC: 11 AN: 10620

Middle Eastern (MID) AF: 0.127 AC: 37 AN: 292

European-Non Finnish (NFE) AF: 0.0107 AC: 729 AN: 68022

Other (OTH) AF: 0.0735 AC: 155 AN: 2110

Alfa AF: 0.0381 Hom.: 43

Bravo AF: 0.0704

Asia WGS AF: 0.168 AC: 585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.48
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs4835929; hg19: chr5-127054278;