rs1048466

Variant names:

• chr12-442384-G-A
• rs1048466
• NM_032358.4:c.*464G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-442384-G-A
• chr12-442384-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032358.4(CCDC77):​c.*464G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 153,304 control chromosomes in the GnomAD database, including 4,911 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 0.25 (4857 hom., cov: 31)
  • Exomes 𝑓: 0.29 (54 hom.)
• Consequence: CCDC77 NM_032358.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375
• Publications: 21 publications found

Genes affected

CCDC77 (HGNC:28203): (coiled-coil domain containing 77) Located in centrosome. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000303058 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032358.4. 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
	CCDC77	NM_032358.4	MANE Select	c.*464G>A		3_prime_UTR	Exon 13 of 13	NP_115734.1
	CCDC77	NM_001130146.2		c.*464G>A		3_prime_UTR	Exon 12 of 12	NP_001123618.1
	CCDC77	NM_001130147.2		c.*464G>A		3_prime_UTR	Exon 12 of 12	NP_001123619.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC77	ENST00000239830.9	TSL:2 MANE Select	c.*464G>A		3_prime_UTR	Exon 13 of 13	ENSP00000239830.4
	CCDC77	ENST00000537286.1	TSL:3	n.705G>A		splice_region non_coding_transcript_exon	Exon 2 of 2
	CCDC77	ENST00000412006.6	TSL:2	c.*464G>A		3_prime_UTR	Exon 12 of 12	ENSP00000412925.2

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37348 AN: 151860 Hom.: 4854 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.210

GnomAD4 exome AF: 0.293 AC: 388 AN: 1324 Hom.: 54 Cov.: 0 AF XY: 0.284 AC XY: 199 AN XY: 700

African (AFR) AF: 0.00 AC: 0 AN: 6

American (AMR) AF: 0.277 AC: 52 AN: 188

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 5 AN: 18

East Asian (EAS) AF: 0.429 AC: 12 AN: 28

South Asian (SAS) AF: 0.209 AC: 18 AN: 86

European-Finnish (FIN) AF: 0.250 AC: 4 AN: 16

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.304 AC: 283 AN: 932

Other (OTH) AF: 0.280 AC: 14 AN: 50

GnomAD4 genome AF: 0.246 AC: 37372 AN: 151980 Hom.: 4857 Cov.: 31 AF XY: 0.249 AC XY: 18526 AN XY: 74266

African (AFR) AF: 0.197 AC: 8156 AN: 41456

American (AMR) AF: 0.182 AC: 2775 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 670 AN: 3472

East Asian (EAS) AF: 0.306 AC: 1577 AN: 5156

South Asian (SAS) AF: 0.243 AC: 1172 AN: 4816

European-Finnish (FIN) AF: 0.369 AC: 3892 AN: 10542

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18470 AN: 67956

Other (OTH) AF: 0.207 AC: 438 AN: 2112

Alfa AF: 0.250 Hom.: 12935

Bravo AF: 0.229

Asia WGS AF: 0.281 AC: 978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.56
PhyloP100		-0.38
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1048466; hg19: chr12-551550;