chr12-122811747-G-A

Position:

• chr12-122811747-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC62	NM_201435.5	c.1852-1523G>A		intron_variant		ENST00000253079.11	NP_958843.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC62	ENST00000253079.11	c.1852-1523G>A		intron_variant		1	NM_201435.5	ENSP00000253079	P3

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

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.406

Alfa AF: 0.400 Hom.: 1569

Bravo AF: 0.390

Asia WGS AF: 0.505 AC: 1756 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.27

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

Publications

LitVar

Other links and lift over

dbSNP: rs12817488; hg19: chr12-123296294;