rs12309211

Variant names:

• chr12-53710248-G-A
• rs12309211
• NM_020898.3:c.*1696C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-53710248-G-A
• chr12-53710248-G-C

Variant summary

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

The NM_020898.3(CALCOCO1):​c.*1696C>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 0.565 in 152,006 control chromosomes in the GnomAD database, including 24,463 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 (24450 hom., cov: 31)
  • Exomes 𝑓: 0.58 (13 hom.)
• Consequence: CALCOCO1 NM_020898.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 5 publications found

Genes affected

CALCOCO1 (HGNC:29306): (calcium binding and coiled-coil domain 1) Enables several functions, including armadillo repeat domain binding activity; beta-catenin binding activity; and nuclear receptor coactivator activity. Involved in positive regulation of gene expression and positive regulation of transcription, DNA-templated. Located in cytosol and nucleus. [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=-0.5).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020898.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CALCOCO1	NM_020898.3	MANE Select	c.*1696C>T		3_prime_UTR	Exon 15 of 15	NP_065949.1	Q9P1Z2-1
	CALCOCO1	NM_001143682.2		c.*1696C>T		3_prime_UTR	Exon 14 of 14	NP_001137154.1	Q9P1Z2-4
	CALCOCO1	NR_026554.2		n.3742C>T		non_coding_transcript_exon	Exon 14 of 14

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CALCOCO1	ENST00000550804.6	TSL:1 MANE Select	c.*1696C>T		3_prime_UTR	Exon 15 of 15	ENSP00000449960.1	Q9P1Z2-1
	CALCOCO1	ENST00000262059.8	TSL:2	c.*1696C>T		3_prime_UTR	Exon 15 of 15	ENSP00000262059.4	Q9P1Z2-3

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85808 AN: 151810 Hom.: 24414 Cov.: 31

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.538

GnomAD4 exome AF: 0.577 AC: 45 AN: 78 Hom.: 13 Cov.: 0 AF XY: 0.571 AC XY: 24 AN XY: 42

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: 0.620 AC: 31 AN: 50

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.500 AC: 8 AN: 16

Other (OTH) AF: 0.400 AC: 4 AN: 10

GnomAD4 genome AF: 0.565 AC: 85892 AN: 151928 Hom.: 24450 Cov.: 31 AF XY: 0.563 AC XY: 41777 AN XY: 74248

African (AFR) AF: 0.613 AC: 25366 AN: 41392

American (AMR) AF: 0.509 AC: 7775 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 2000 AN: 3470

East Asian (EAS) AF: 0.478 AC: 2466 AN: 5164

South Asian (SAS) AF: 0.479 AC: 2303 AN: 4812

European-Finnish (FIN) AF: 0.561 AC: 5913 AN: 10544

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38155 AN: 67956

Other (OTH) AF: 0.539 AC: 1138 AN: 2110

Alfa AF: 0.556 Hom.: 40210

Bravo AF: 0.565

Asia WGS AF: 0.515 AC: 1790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	15
DANN	Benign	0.80
PhyloP100		1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12309211; hg19: chr12-54104032;