rs245311

Variant names:

• chr5-127830907-A-G
• rs245311
• NM_001317938.2:c.411+32745A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-127830907-A-G
• chr5-127830907-A-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+32745A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,156 control chromosomes in the GnomAD database, including 6,787 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 0.30 (6787 hom., cov: 33)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC192	NM_001317938.2	c.411+32745A>G		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+32745A>G		intron_variant	Intron 5 of 6	5	NM_001317938.2	ENSP00000490579.2
CCDC192	ENST00000706942.1	c.468+32745A>G		intron_variant	Intron 5 of 6			ENSP00000516662.1

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44968 AN: 152038 Hom.: 6789 Cov.: 33

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.296 AC: 44982 AN: 152156 Hom.: 6787 Cov.: 33 AF XY: 0.298 AC XY: 22181 AN XY: 74378

African (AFR) AF: 0.235 AC: 9738 AN: 41506

American (AMR) AF: 0.332 AC: 5079 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1338 AN: 3468

East Asian (EAS) AF: 0.411 AC: 2129 AN: 5182

South Asian (SAS) AF: 0.451 AC: 2178 AN: 4824

European-Finnish (FIN) AF: 0.284 AC: 3001 AN: 10568

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20538 AN: 68000

Other (OTH) AF: 0.332 AC: 701 AN: 2112

Alfa AF: 0.306 Hom.: 2456

Bravo AF: 0.298

Asia WGS AF: 0.435 AC: 1511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.75
DANN	Benign	0.49
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs245311; hg19: chr5-127166599;