17-81665212-A-T

Variant names:

• chr17-81665212-A-T
• NM_001039842.3:c.433T>A
• OXLD1 p.Cys145Ser

Variant summary

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

The NM_001039842.3(OXLD1):​c.433T>A​(p.Cys145Ser) variant causes a missense 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. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C145F) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: OXLD1 NM_001039842.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 0 publications found

Genes affected

OXLD1 (HGNC:27901): (oxidoreductase like domain containing 1)

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 (MetaRNN=0.021178931).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039842.3. 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
	OXLD1	NM_001039842.3	MANE Select	c.433T>A	p.Cys145Ser	missense	Exon 2 of 2	NP_001034931.1	Q5BKU9
	OXLD1	NM_001304994.2		c.403T>A	p.Cys135Ser	missense	Exon 2 of 2	NP_001291923.1
	OXLD1	NM_001304995.2		c.*395T>A		3_prime_UTR	Exon 2 of 2	NP_001291924.1	I3L208

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OXLD1	ENST00000374741.4	TSL:1 MANE Select	c.433T>A	p.Cys145Ser	missense	Exon 2 of 2	ENSP00000363873.3	Q5BKU9
	OXLD1	ENST00000934282.1		c.421T>A	p.Cys141Ser	missense	Exon 2 of 2	ENSP00000604341.1
	OXLD1	ENST00000571503.1	TSL:2	c.*395T>A		3_prime_UTR	Exon 2 of 2	ENSP00000466256.1	I3L208

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.068
BayesDel_addAF	Benign	-0.37	T
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.027
DANN	Benign	0.54
DEOGEN2	Benign	0.0040	T
Eigen	Benign	-1.8
Eigen_PC	Benign	-1.8
FATHMM_MKL	Benign	0.042	N
LIST_S2	Benign	0.22	T
M_CAP	Benign	0.0011	T
MetaRNN	Benign	0.021	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-0.97	N
PhyloP100		-1.9
PrimateAI	Benign	0.25	T
PROVEAN	Benign	1.6	N
REVEL	Benign	0.12
Sift	Benign	0.81	T
Sift4G	Benign	1.0	T
Varity_R		0.077
gMVP		0.33

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr17-79632242;