rs969697913

Variant names:

• chr10-59238654-A-G
• rs969697913
• NM_032439.4:c.545A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-59238654-A-G
• chr10-59238654-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_032439.4(PHYHIPL):​c.545A>G​(p.Lys182Arg) 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. 14/21 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. K182M) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PHYHIPL NM_032439.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.62

Genes affected

PHYHIPL (HGNC:29378): (phytanoyl-CoA 2-hydroxylase interacting protein like) Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.09282571).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHYHIPL	NM_032439.4	c.545A>G	p.Lys182Arg	missense_variant	Exon 4 of 5	ENST00000373880.9	NP_115815.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHYHIPL	ENST00000373880.9	c.545A>G	p.Lys182Arg	missense_variant	Exon 4 of 5	1	NM_032439.4	ENSP00000362987.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.071
BayesDel_addAF	Benign	-0.24	T
BayesDel_noAF	Benign	-0.58
CADD	Benign	20
DANN	Benign	0.93
DEOGEN2	Benign	0.028	T;.
Eigen	Benign	-0.32
Eigen_PC	Benign	-0.060
FATHMM_MKL	Uncertain	0.84	D
LIST_S2	Benign	0.81	T;T
M_CAP	Benign	0.0045	T
MetaRNN	Benign	0.093	T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.12	N;.
PrimateAI	Uncertain	0.74	T
PROVEAN	Benign	-0.44	N;N
REVEL	Benign	0.092
Sift	Benign	0.64	T;T
Sift4G	Benign	0.78	T;T
Polyphen		0.0010	B;B
Vest4		0.26
MutPred		0.35		Loss of methylation at K182 (P = 0.035);.;
MVP		0.055
MPC		0.42
ClinPred		0.72	D
GERP RS		5.7
Varity_R		0.21
gMVP		0.34

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: rs969697913; hg19: chr10-60998414;