rs10491253

chr5-127884881-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001317938.2(CCDC192):c.535+9220G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0341 in 152,018 control chromosomes in the GnomAD database, including 202 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 0.034 (202 hom., cov: 32)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC192	NM_001317938.2	c.535+9220G>T		intron_variant		ENST00000514853.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC192	ENST00000514853.5	c.535+9220G>T		intron_variant		5	NM_001317938.2	A2
CCDC192	ENST00000706942.1	c.592+9220G>T		intron_variant				P4

Frequencies

GnomAD3 genomes AF: 0.0342 AC: 5193 AN: 151900 Hom.: 202 Cov.: 32

Gnomad AFR AF: 0.0965

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0252

Gnomad ASJ AF: 0.0591

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00583

Gnomad FIN AF: 0.0000946

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.00681

Gnomad OTH AF: 0.0437

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

GnomAD4 genome AF: 0.0341 AC: 5190 AN: 152018 Hom.: 202 Cov.: 32 AF XY: 0.0333 AC XY: 2473 AN XY: 74304

Gnomad4 AFR AF: 0.0962

Gnomad4 AMR AF: 0.0252

Gnomad4 ASJ AF: 0.0591

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00583

Gnomad4 FIN AF: 0.0000946

Gnomad4 NFE AF: 0.00681

Gnomad4 OTH AF: 0.0437

Alfa AF: 0.0137 Hom.: 40

Bravo AF: 0.0380

Asia WGS AF: 0.00866 AC: 31 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.2
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491253; hg19: chr5-127220573;