chr7-87359723-G-T

Variant names:

• chr7-87359723-G-T
• rs802026
• ENST00000412227.6:c.*369G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001243745.3(CROT):​c.*369G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CROT NM_001243745.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.745
• Publications: 6 publications found

Genes affected

CROT (HGNC:2366): (carnitine O-octanoyltransferase) This gene encodes a member of the carnitine/choline acetyltransferase family. The encoded protein converts 4,8-dimethylnonanoyl-CoA to its corresponding carnitine ester. This transesterification occurs in the peroxisome and is necessary for transport of medium- and long- chain acyl-CoA molecules out of the peroxisome to the cytosol and mitochondria. The protein thus plays a role in lipid metabolism and fatty acid beta-oxidation. Alternatively spliced transcript variants have been described.[provided by RefSeq, Jan 2009]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001243745.3. 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
	CROT	NM_021151.4	MANE Select	c.240+393G>T		intron	N/A	NP_066974.2
	CROT	NM_001243745.3		c.*369G>T		3_prime_UTR	Exon 4 of 4	NP_001230674.1	Q9UKG9-2
	CROT	NM_001143935.2		c.324+393G>T		intron	N/A	NP_001137407.1	Q9UKG9-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CROT	ENST00000412227.6	TSL:1	c.*369G>T		3_prime_UTR	Exon 4 of 4	ENSP00000404867.2	Q9UKG9-2
	CROT	ENST00000331536.8	TSL:1 MANE Select	c.240+393G>T		intron	N/A	ENSP00000331981.4	Q9UKG9-1
	CROT	ENST00000419147.6	TSL:2	c.324+393G>T		intron	N/A	ENSP00000413575.2	Q9UKG9-3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 861612 Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0 AN XY: 399240

African (AFR) AF: 0.00 AC: 0 AN: 16008

American (AMR) AF: 0.00 AC: 0 AN: 1710

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5718

East Asian (EAS) AF: 0.00 AC: 0 AN: 4418

South Asian (SAS) AF: 0.00 AC: 0 AN: 19228

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2036

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1732

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 781620

Other (OTH) AF: 0.00 AC: 0 AN: 29142

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 4939

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.49
PhyloP100		0.74

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: rs802026; hg19: chr7-86989039;