chr5-41870704-C-T

Position:

• chr5-41870704-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

The ENST00000510509.1(OXCT1-AS1):​n.487C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00526 in 384,418 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0099 (26 hom., cov: 33)
  • Exomes 𝑓: 0.0022 (2 hom.)
• Consequence: OXCT1-AS1 ENST00000510509.1 non_coding_transcript_exon
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.33

Genes affected

OXCT1-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 5-41870704-C-T is Benign according to our data. Variant chr5-41870704-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 369475.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0099 (1507/152296) while in subpopulation AFR AF= 0.0306 (1271/41564). AF 95% confidence interval is 0.0292. There are 26 homozygotes in gnomad4. There are 711 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 26 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OXCT1-AS1	NR_046635.1	n.256-62C>T		intron_variant
LOC102723752	XR_007058750.1	n.41+1671C>T		intron_variant
LOC102723752	XR_427695.4	n.80+1632C>T		intron_variant
LOC102723752	XR_925956.4	n.6415+1102C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OXCT1-AS1	ENST00000510509.1	n.487C>T		non_coding_transcript_exon_variant	2/2	3
OXCT1-AS1	ENST00000654321.1	n.680C>T		non_coding_transcript_exon_variant	2/2
OXCT1-AS1	ENST00000508458.2	n.256-62C>T		intron_variant		3
ENSG00000286164	ENST00000651810.1	n.98+1632C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.00986 AC: 1501 AN: 152180 Hom.: 25 Cov.: 33

Gnomad AFR AF: 0.0305

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.00484

Gnomad ASJ AF: 0.00662

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000828

Gnomad FIN AF: 0.0000943

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00115

Gnomad OTH AF: 0.00957

GnomAD4 exome AF: 0.00222 AC: 516 AN: 232122 Hom.: 2 Cov.: 0 AF XY: 0.00209 AC XY: 264 AN XY: 126222

Gnomad4 AFR exome AF: 0.0323

Gnomad4 AMR exome AF: 0.00495

Gnomad4 ASJ exome AF: 0.00584

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000401

Gnomad4 FIN exome AF: 0.000774

Gnomad4 NFE exome AF: 0.00106

Gnomad4 OTH exome AF: 0.00377

GnomAD4 genome AF: 0.00990 AC: 1507 AN: 152296 Hom.: 26 Cov.: 33 AF XY: 0.00955 AC XY: 711 AN XY: 74472

Gnomad4 AFR AF: 0.0306

Gnomad4 AMR AF: 0.00483

Gnomad4 ASJ AF: 0.00662

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000829

Gnomad4 FIN AF: 0.0000943

Gnomad4 NFE AF: 0.00115

Gnomad4 OTH AF: 0.00947

Alfa AF: 0.00556 Hom.: 0

Bravo AF: 0.0110

Asia WGS AF: 0.00260 AC: 9 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Succinyl-CoA acetoacetate transferase deficiency Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.50
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs138037654; hg19: chr5-41870806;