NM_031938.7:c.732A>C

Variant names:

• chr11-112194751-A-C
• rs149790013
• NM_031938.7:c.732A>C

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_031938.7(BCO2):​c.732A>C​(p.Pro244Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00271 in 1,587,752 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0019 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0028 (11 hom.)
• Consequence: BCO2 NM_031938.7 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.45
• Publications: 0 publications found

Genes affected

BCO2 (HGNC:18503): (beta-carotene oxygenase 2) This gene encodes an enzyme which oxidizes carotenoids such as beta-carotene during the biosynthesis of vitamin A. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

ACMG classification

Our verdict: Benign. The variant received -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 11-112194751-A-C is Benign according to our data. Variant chr11-112194751-A-C is described in ClinVar as Likely_benign. ClinVar VariationId is 2642372.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=1.45 with no splicing effect.
• BS2: High Homozygotes in GnomAdExome4 at 11 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031938.7. 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
	BCO2	NM_031938.7	MANE Select	c.732A>C	p.Pro244Pro	synonymous	Exon 5 of 12	NP_114144.5
	BCO2	NM_001037290.4		c.630A>C	p.Pro210Pro	synonymous	Exon 5 of 12	NP_001032367.3	Q9BYV7-2
	BCO2	NM_001256397.3		c.630A>C	p.Pro210Pro	synonymous	Exon 5 of 12	NP_001243326.2	Q9BYV7-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCO2	ENST00000357685.11	TSL:1 MANE Select	c.732A>C	p.Pro244Pro	synonymous	Exon 5 of 12	ENSP00000350314.5	Q9BYV7-1
	BCO2	ENST00000438022.5	TSL:1	c.630A>C	p.Pro210Pro	synonymous	Exon 5 of 12	ENSP00000414843.1	Q9BYV7-2
	BCO2	ENST00000531169.5	TSL:1	c.630A>C	p.Pro210Pro	synonymous	Exon 5 of 13	ENSP00000437053.1	Q9BYV7-2

Frequencies

GnomAD3 genomes AF: 0.00191 AC: 291 AN: 152174 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000265

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00137

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.00217

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00313

Gnomad OTH AF: 0.00239

GnomAD2 exomes AF: 0.00275 AC: 670 AN: 243892 AF XY: 0.00308

Gnomad AFR exome AF: 0.000502

Gnomad AMR exome AF: 0.00121

Gnomad ASJ exome AF: 0.00101

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00251

Gnomad NFE exome AF: 0.00393

Gnomad OTH exome AF: 0.00284

GnomAD4 exome AF: 0.00279 AC: 4007 AN: 1435460 Hom.: 11 Cov.: 27 AF XY: 0.00285 AC XY: 2037 AN XY: 715430

African (AFR) AF: 0.000399 AC: 13 AN: 32564

American (AMR) AF: 0.00109 AC: 47 AN: 43084

Ashkenazi Jewish (ASJ) AF: 0.00147 AC: 38 AN: 25900

East Asian (EAS) AF: 0.000101 AC: 4 AN: 39440

South Asian (SAS) AF: 0.00387 AC: 327 AN: 84416

European-Finnish (FIN) AF: 0.00296 AC: 158 AN: 53368

Middle Eastern (MID) AF: 0.00105 AC: 6 AN: 5716

European-Non Finnish (NFE) AF: 0.00298 AC: 3253 AN: 1091402

Other (OTH) AF: 0.00270 AC: 161 AN: 59570

GnomAD4 genome AF: 0.00190 AC: 290 AN: 152292 Hom.: 0 Cov.: 32 AF XY: 0.00175 AC XY: 130 AN XY: 74482

African (AFR) AF: 0.000265 AC: 11 AN: 41562

American (AMR) AF: 0.00131 AC: 20 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00202 AC: 7 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.00228 AC: 11 AN: 4824

European-Finnish (FIN) AF: 0.00217 AC: 23 AN: 10622

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00313 AC: 213 AN: 68016

Other (OTH) AF: 0.00236 AC: 5 AN: 2116

Alfa AF: 0.00230 Hom.: 1

Bravo AF: 0.00180

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.67
PhyloP100		1.5
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs149790013; hg19: chr11-112065474;