12-122811747-G-A

Variant names:

• chr12-122811747-G-A
• rs12817488
• NM_201435.5:c.1852-1523G>A

Variant summary

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

The NM_201435.5(CCDC62):​c.1852-1523G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 146,608 control chromosomes in the GnomAD database, including 12,250 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 0.40 (12250 hom., cov: 21)
• Consequence: CCDC62 NM_201435.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 40 publications found

Genes affected

CCDC62 (HGNC:30723): (coiled-coil domain containing 62) Enables estrogen receptor binding activity and nuclear receptor coactivator activity. Involved in cellular response to estradiol stimulus and positive regulation of transcription by RNA polymerase II. Located in nucleoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_201435.5. 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
	CCDC62	NM_201435.5	MANE Select	c.1852-1523G>A		intron	N/A	NP_958843.2
	CCDC62	NR_027918.3		n.1951-1523G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC62	ENST00000253079.11	TSL:1 MANE Select	c.1852-1523G>A		intron	N/A	ENSP00000253079.6
	CCDC62	ENST00000392440.3	TSL:1	c.1297-1523G>A		intron	N/A	ENSP00000376235.3
	CCDC62	ENST00000392441.8	TSL:5	c.1852-1523G>A		intron	N/A	ENSP00000376236.4

Frequencies

GnomAD3 genomes AF: 0.398 AC: 58340 AN: 146510 Hom.: 12238 Cov.: 21

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.333

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.398 AC: 58368 AN: 146608 Hom.: 12250 Cov.: 21 AF XY: 0.399 AC XY: 28410 AN XY: 71148

African (AFR) AF: 0.260 AC: 10302 AN: 39676

American (AMR) AF: 0.447 AC: 6472 AN: 14480

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1360 AN: 3442

East Asian (EAS) AF: 0.533 AC: 2535 AN: 4754

South Asian (SAS) AF: 0.462 AC: 2133 AN: 4616

European-Finnish (FIN) AF: 0.409 AC: 3870 AN: 9464

Middle Eastern (MID) AF: 0.350 AC: 100 AN: 286

European-Non Finnish (NFE) AF: 0.456 AC: 30550 AN: 66974

Other (OTH) AF: 0.406 AC: 817 AN: 2014

Alfa AF: 0.650 Hom.: 8113

Bravo AF: 0.390

Asia WGS AF: 0.505 AC: 1756 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.27
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs12817488; hg19: chr12-123296294;