rs7513934

Variant names:

• chr1-52352516-G-A
• rs7513934
• NM_001330585.2:c.*709C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 31 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CC2D1B	NM_001330585.2	c.*709C>T		3_prime_UTR_variant	Exon 25 of 25	ENST00000284376.8	NP_001317514.1
CC2D1B	NM_032449.3	c.*1003C>T		3_prime_UTR_variant	Exon 24 of 24		NP_115825.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CC2D1B	ENST00000284376.8	c.*709C>T		3_prime_UTR_variant	Exon 25 of 25	5	NM_001330585.2	ENSP00000284376.3

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.458 AC: 195 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.750 AC: 3 AN: 4

Other (OTH) AF: 1.00 AC: 4 AN: 4

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

African (AFR) AF: 0.853 AC: 35408 AN: 41512

American (AMR) AF: 0.408 AC: 6229 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1888 AN: 3472

East Asian (EAS) AF: 0.160 AC: 831 AN: 5178

South Asian (SAS) AF: 0.523 AC: 2510 AN: 4802

European-Finnish (FIN) AF: 0.435 AC: 4588 AN: 10536

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34178 AN: 67948

Other (OTH) AF: 0.528 AC: 1109 AN: 2102

Alfa AF: 0.524 Hom.: 38748

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
PhyloP100		-0.99
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: rs7513934; hg19: chr1-52818188; COSMIC: COSV52560148; COSMIC: COSV52560148;