chr5-127839739-G-A

Variant names:

• chr5-127839739-G-A
• rs6874357
• NM_001317938.2:c.412-35799G>A

Variant summary

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

The NM_001317938.2(CCDC192):​c.412-35799G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,802 control chromosomes in the GnomAD database, including 8,479 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 0.32 (8479 hom., cov: 31)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342
• Publications: 2 publications found

Genes affected

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

ENSG00000250603 (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 (NFE) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC192	NM_001317938.2	c.412-35799G>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.412-35799G>A		intron_variant	Intron 5 of 6	5	NM_001317938.2	ENSP00000490579.2
CCDC192	ENST00000706942.1	c.469-35799G>A		intron_variant	Intron 5 of 6			ENSP00000516662.1
ENSG00000250603	ENST00000507509.1	n.192-1057C>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48596 AN: 151684 Hom.: 8474 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.320 AC: 48609 AN: 151802 Hom.: 8479 Cov.: 31 AF XY: 0.318 AC XY: 23603 AN XY: 74194

African (AFR) AF: 0.191 AC: 7891 AN: 41408

American (AMR) AF: 0.298 AC: 4537 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1088 AN: 3466

East Asian (EAS) AF: 0.255 AC: 1314 AN: 5158

South Asian (SAS) AF: 0.194 AC: 931 AN: 4808

European-Finnish (FIN) AF: 0.426 AC: 4467 AN: 10494

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27175 AN: 67932

Other (OTH) AF: 0.317 AC: 665 AN: 2096

Alfa AF: 0.369 Hom.: 6364

Bravo AF: 0.307

Asia WGS AF: 0.200 AC: 699 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.45
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs6874357; hg19: chr5-127175431;