rs10463833

Variant names:

• chr5-127786620-G-A
• rs10463833
• NM_001317938.2:c.223-10483G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-127786620-G-A
• chr5-127786620-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.223-10483G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0829 in 753,072 control chromosomes in the GnomAD database, including 8,134 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 0.15 (3752 hom., cov: 32)
  • Exomes 𝑓: 0.067 (4382 hom.)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.80
• Publications: 3 publications found

Genes affected

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

CUL1P1 (HGNC:49567): (cullin 1 pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC192	NM_001317938.2	MANE Select	c.223-10483G>A		intron	N/A	NP_001304867.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC192	ENST00000514853.5	TSL:5 MANE Select	c.223-10483G>A		intron	N/A	ENSP00000490579.2
	CUL1P1	ENST00000509510.1	TSL:6	n.423C>T		non_coding_transcript_exon	Exon 1 of 1
	CCDC192	ENST00000706942.1		c.280-10483G>A		intron	N/A	ENSP00000516662.1

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22094 AN: 152062 Hom.: 3743 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.0841

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0121

Gnomad OTH AF: 0.130

GnomAD4 exome AF: 0.0670 AC: 40264 AN: 600892 Hom.: 4382 Cov.: 0 AF XY: 0.0619 AC XY: 20273 AN XY: 327518

African (AFR) AF: 0.391 AC: 6720 AN: 17192

American (AMR) AF: 0.225 AC: 9519 AN: 42332

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 2150 AN: 20086

East Asian (EAS) AF: 0.263 AC: 9316 AN: 35370

South Asian (SAS) AF: 0.0760 AC: 5195 AN: 68360

European-Finnish (FIN) AF: 0.00262 AC: 127 AN: 48490

Middle Eastern (MID) AF: 0.0812 AC: 321 AN: 3952

European-Non Finnish (NFE) AF: 0.0134 AC: 4456 AN: 333672

Other (OTH) AF: 0.0782 AC: 2460 AN: 31438

GnomAD4 genome AF: 0.146 AC: 22146 AN: 152180 Hom.: 3752 Cov.: 32 AF XY: 0.145 AC XY: 10784 AN XY: 74426

African (AFR) AF: 0.396 AC: 16405 AN: 41472

American (AMR) AF: 0.161 AC: 2456 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0963 AC: 334 AN: 3470

East Asian (EAS) AF: 0.269 AC: 1393 AN: 5176

South Asian (SAS) AF: 0.0842 AC: 406 AN: 4824

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

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0121 AC: 821 AN: 68018

Other (OTH) AF: 0.132 AC: 278 AN: 2106

Alfa AF: 0.0591 Hom.: 198

Bravo AF: 0.171

Asia WGS AF: 0.209 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	2.1
DANN	Benign	0.77
PhyloP100		1.8
Mutation Taster		=88/12	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10463833; hg19: chr5-127122312; COSMIC: COSV72618160;