rs7513934

chr1-52352516-G-A

Variant summary

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

The NM_001330585.2(CC2D1B):c.*709C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 152,462 control chromosomes in the GnomAD database, including 27,913 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 0.57 (27858 hom., cov: 32)
  • Exomes 𝑓: 0.47 (55 hom.)
• Consequence: CC2D1B NM_001330585.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995

Genes affected

CC2D1B (HGNC:29386): (coiled-coil and C2 domain containing 1B) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Located in nucleoplasm. [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=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CC2D1B	NM_001330585.2	c.*709C>T		3_prime_UTR_variant	25/25	ENST00000284376.8
CC2D1B	NM_032449.3	c.*1003C>T		3_prime_UTR_variant	24/24

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CC2D1B	ENST00000284376.8	c.*709C>T		3_prime_UTR_variant	25/25	5	NM_001330585.2	P1

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87193 AN: 151910 Hom.: 27810 Cov.: 32

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.531

GnomAD4 exome AF: 0.465 AC: 202 AN: 434 Hom.: 55 Cov.: 0 AF XY: 0.504 AC XY: 132 AN XY: 262

Gnomad4 FIN exome AF: 0.458

Gnomad4 NFE exome AF: 0.750

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.574 AC: 87292 AN: 152028 Hom.: 27858 Cov.: 32 AF XY: 0.564 AC XY: 41924 AN XY: 74318

Gnomad4 AFR AF: 0.853

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.528

Alfa AF: 0.517 Hom.: 27051

Bravo AF: 0.581

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	5.1
Dann	Benign	0.28

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: rs7513934; hg19: chr1-52818188; COSMIC: COSV52560148; COSMIC: COSV52560148;