5-116051538-T-A

Position:

• chr5-116051538-T-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001195581.2(ARL14EPL):​c.73T>A​(p.Cys25Ser) 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. 12/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ARL14EPL NM_001195581.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323

Genes affected

ARL14EPL (HGNC:44201): (ADP ribosylation factor like GTPase 14 effector protein like)

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 (MetaRNN=0.057767957).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARL14EPL	NM_001195581.2	c.73T>A	p.Cys25Ser	missense_variant	2/4	ENST00000686077.1
ARL14EPL	NM_001393974.1	c.73T>A	p.Cys25Ser	missense_variant	3/5
ARL14EPL	NM_001385024.1	c.-102-2476T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARL14EPL	ENST00000686077.1	c.73T>A	p.Cys25Ser	missense_variant	2/4		NM_001195581.2	P1
ARL14EPL	ENST00000601302.3	c.73T>A	p.Cys25Ser	missense_variant	3/5	5		P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.074
BayesDel_addAF	Benign	-0.25	T
BayesDel_noAF	Benign	-0.60
CADD	Benign	3.3
DANN	Benign	0.89
DEOGEN2	Benign	0.0052	T;T
FATHMM_MKL	Benign	0.025	N
M_CAP	Benign	0.0089	T
MetaRNN	Benign	0.058	T;T
MutationAssessor	Benign	0.69	N;N
PrimateAI	Benign	0.32	T
Sift4G	Benign	0.69	T;T
Vest4		0.13
MVP		0.56
GERP RS		0.46
Varity_R		0.089
gMVP		0.19

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-115387235;