5-127830941-C-T

Variant names:

• chr5-127830941-C-T
• rs245310
• NM_001317938.2:c.411+32779C>T

Variant summary

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

The NM_001317938.2(CCDC192):​c.411+32779C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 152,022 control chromosomes in the GnomAD database, including 9,067 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 0.34 (9067 hom., cov: 33)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368
• Publications: 3 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC192	NM_001317938.2	c.411+32779C>T		intron_variant	Intron 5 of 6	ENST00000514853.5	NP_001304867.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC192	ENST00000514853.5	c.411+32779C>T		intron_variant	Intron 5 of 6	5	NM_001317938.2	ENSP00000490579.2
CCDC192	ENST00000706942.1	c.468+32779C>T		intron_variant	Intron 5 of 6			ENSP00000516662.1

Frequencies

GnomAD3 genomes AF: 0.342 AC: 52024 AN: 151904 Hom.: 9054 Cov.: 33

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.343 AC: 52076 AN: 152022 Hom.: 9067 Cov.: 33 AF XY: 0.344 AC XY: 25566 AN XY: 74304

African (AFR) AF: 0.398 AC: 16490 AN: 41442

American (AMR) AF: 0.347 AC: 5307 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1338 AN: 3470

East Asian (EAS) AF: 0.412 AC: 2129 AN: 5172

South Asian (SAS) AF: 0.456 AC: 2200 AN: 4820

European-Finnish (FIN) AF: 0.284 AC: 2997 AN: 10542

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20567 AN: 67978

Other (OTH) AF: 0.363 AC: 766 AN: 2112

Alfa AF: 0.297 Hom.: 2287

Bravo AF: 0.351

Asia WGS AF: 0.455 AC: 1582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.065
DANN	Benign	0.53
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs245310; hg19: chr5-127166633;