NM_001317938.2:c.535+12946T>C

Variant names:

• chr5-127888607-T-C
• rs10491254
• NM_001317938.2:c.535+12946T>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.535+12946T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0502 in 152,248 control chromosomes in the GnomAD database, including 505 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 0.050 (505 hom., cov: 31)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 0 publications found

Genes affected

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

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 (AFR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC192	NM_001317938.2	c.535+12946T>C		intron_variant	Intron 6 of 6	ENST00000514853.5	NP_001304867.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC192	ENST00000514853.5	c.535+12946T>C		intron_variant	Intron 6 of 6	5	NM_001317938.2	ENSP00000490579.2
CCDC192	ENST00000706942.1	c.592+12946T>C		intron_variant	Intron 6 of 6			ENSP00000516662.1

Frequencies

GnomAD3 genomes AF: 0.0501 AC: 7625 AN: 152130 Hom.: 501 Cov.: 31

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0306

Gnomad ASJ AF: 0.0590

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00601

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.00703

Gnomad OTH AF: 0.0554

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

GnomAD4 genome AF: 0.0502 AC: 7644 AN: 152248 Hom.: 505 Cov.: 31 AF XY: 0.0492 AC XY: 3663 AN XY: 74448

African (AFR) AF: 0.152 AC: 6311 AN: 41516

American (AMR) AF: 0.0305 AC: 467 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0590 AC: 205 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5188

South Asian (SAS) AF: 0.00601 AC: 29 AN: 4824

European-Finnish (FIN) AF: 0.0000942 AC: 1 AN: 10618

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.00703 AC: 478 AN: 68020

Other (OTH) AF: 0.0553 AC: 117 AN: 2116

Alfa AF: 0.0278 Hom.: 52

Bravo AF: 0.0566

Asia WGS AF: 0.0170 AC: 59 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	4.7
DANN	Benign	0.68
PhyloP100		0.032

Splicing

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

Other links and lift over

dbSNP: rs10491254; hg19: chr5-127224299;