rs1515641

Variant names:

• chr5-127803924-G-A
• rs1515641
• NM_001317938.2:c.411+5762G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-127803924-G-A
• chr5-127803924-G-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+5762G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0568 in 152,190 control chromosomes in the GnomAD database, including 558 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 0.057 (558 hom., cov: 32)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.95
• Publications: 5 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 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+5762G>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+5762G>A		intron	N/A	ENSP00000490579.2	A0A9S7N7Z0
	CCDC192	ENST00000706942.1		c.468+5762G>A		intron	N/A	ENSP00000516662.1	P0DO97

Frequencies

GnomAD3 genomes AF: 0.0568 AC: 8645 AN: 152072 Hom.: 557 Cov.: 32

Gnomad AFR AF: 0.0891

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0954

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.0768

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0108

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0568 AC: 8652 AN: 152190 Hom.: 558 Cov.: 32 AF XY: 0.0595 AC XY: 4425 AN XY: 74424

African (AFR) AF: 0.0889 AC: 3692 AN: 41508

American (AMR) AF: 0.127 AC: 1936 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0954 AC: 331 AN: 3468

East Asian (EAS) AF: 0.268 AC: 1387 AN: 5168

South Asian (SAS) AF: 0.0770 AC: 371 AN: 4816

European-Finnish (FIN) AF: 0.00104 AC: 11 AN: 10614

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0108 AC: 735 AN: 68004

Other (OTH) AF: 0.0719 AC: 152 AN: 2114

Alfa AF: 0.0323 Hom.: 736

Bravo AF: 0.0689

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.0030
DANN	Benign	0.44
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs1515641; hg19: chr5-127139616;