rs698172

Variant names:

• chr5-127819235-G-A
• rs698172
• NM_001317938.2:c.411+21073G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-127819235-G-A
• chr5-127819235-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.411+21073G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,966 control chromosomes in the GnomAD database, including 9,391 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 0.33 (9391 hom., cov: 32)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001317938.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC192	NM_001317938.2	MANE Select	c.411+21073G>A		intron	N/A	NP_001304867.2	A0A9S7N7Z0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC192	ENST00000514853.5	TSL:5 MANE Select	c.411+21073G>A		intron	N/A	ENSP00000490579.2	A0A9S7N7Z0
	CCDC192	ENST00000706942.1		c.468+21073G>A		intron	N/A	ENSP00000516662.1	P0DO97

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50811 AN: 151848 Hom.: 9396 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.334 AC: 50813 AN: 151966 Hom.: 9391 Cov.: 32 AF XY: 0.335 AC XY: 24875 AN XY: 74274

African (AFR) AF: 0.165 AC: 6841 AN: 41464

American (AMR) AF: 0.381 AC: 5815 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1255 AN: 3470

East Asian (EAS) AF: 0.455 AC: 2344 AN: 5156

South Asian (SAS) AF: 0.470 AC: 2255 AN: 4802

European-Finnish (FIN) AF: 0.348 AC: 3676 AN: 10556

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27403 AN: 67942

Other (OTH) AF: 0.365 AC: 771 AN: 2110

Alfa AF: 0.384 Hom.: 6876

Bravo AF: 0.332

Asia WGS AF: 0.443 AC: 1540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs698172; hg19: chr5-127154927;