rs6864687

Variant names:

• chr5-127860374-G-A
• rs6864687
• NM_001317938.2:c.412-15164G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-127860374-G-A
• chr5-127860374-G-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.412-15164G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 151,852 control chromosomes in the GnomAD database, including 11,853 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 0.39 (11853 hom., cov: 32)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.83
• Publications: 2 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=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC192	NM_001317938.2	c.412-15164G>A		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.412-15164G>A		intron_variant	Intron 5 of 6	5	NM_001317938.2	ENSP00000490579.2
CCDC192	ENST00000706942.1	c.469-15164G>A		intron_variant	Intron 5 of 6			ENSP00000516662.1

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59445 AN: 151734 Hom.: 11842 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.392 AC: 59478 AN: 151852 Hom.: 11853 Cov.: 32 AF XY: 0.392 AC XY: 29116 AN XY: 74192

African (AFR) AF: 0.344 AC: 14236 AN: 41428

American (AMR) AF: 0.423 AC: 6456 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1302 AN: 3470

East Asian (EAS) AF: 0.538 AC: 2771 AN: 5154

South Asian (SAS) AF: 0.281 AC: 1354 AN: 4818

European-Finnish (FIN) AF: 0.426 AC: 4482 AN: 10512

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27505 AN: 67922

Other (OTH) AF: 0.390 AC: 819 AN: 2100

Alfa AF: 0.399 Hom.: 54941

Bravo AF: 0.391

Asia WGS AF: 0.374 AC: 1301 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	13
DANN	Benign	0.80
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs6864687; hg19: chr5-127196066;