rs11060112

Positions:

• chr12-122807956-A-C
• chr12-122807956-A-G
• chr12-122807956-A-T

Variant summary

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

The NM_201435.5(CCDC62):​c.1851+1661A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,148 control chromosomes in the GnomAD database, including 3,380 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 0.19 (3380 hom., cov: 32)
• Consequence: CCDC62 NM_201435.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC62	NM_201435.5	c.1851+1661A>C		intron_variant		ENST00000253079.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC62	ENST00000253079.11	c.1851+1661A>C		intron_variant		1	NM_201435.5	P3

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28973 AN: 152030 Hom.: 3381 Cov.: 32

Gnomad AFR AF: 0.0626

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.0766

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.190 AC: 28957 AN: 152148 Hom.: 3380 Cov.: 32 AF XY: 0.185 AC XY: 13758 AN XY: 74384

Gnomad4 AFR AF: 0.0625

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.0763

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.205

Alfa AF: 0.216 Hom.: 2006

Bravo AF: 0.186

Asia WGS AF: 0.114 AC: 399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.81

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

Publications

LitVar

Other links and lift over

dbSNP: rs11060112; hg19: chr12-123292503;