7-87359723-G-T

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -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

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

Verdict is Likely_benign. Variant got -2 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CROT	NM_021151.4	c.240+393G>T		intron_variant	Intron 4 of 17	ENST00000331536.8	NP_066974.2
CROT	NM_001243745.3	c.*369G>T		3_prime_UTR_variant	Exon 4 of 4		NP_001230674.1
CROT	NM_001143935.2	c.324+393G>T		intron_variant	Intron 5 of 18		NP_001137407.1
CROT	XM_011516337.4	c.240+393G>T		intron_variant	Intron 4 of 17		XP_011514639.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CROT	ENST00000412227.6	c.*369G>T		3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000404867.2
CROT	ENST00000331536.8	c.240+393G>T		intron_variant	Intron 4 of 17	1	NM_021151.4	ENSP00000331981.4
CROT	ENST00000419147.6	c.324+393G>T		intron_variant	Intron 5 of 18	2		ENSP00000413575.2
CROT	ENST00000442291.1	c.240+393G>T		intron_variant	Intron 3 of 16	5		ENSP00000411983.1

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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: rs802026; hg19: chr7-86989039;