rs518357

Variant names:

• chr11-30219282-C-T
• rs518357
• ENST00000527819.2:n.471-62429G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000527819.2(ARL14EP-DT):​n.471-62429G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,970 control chromosomes in the GnomAD database, including 17,351 homozygotes. 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: 𝑓 0.48 (17351 hom., cov: 32)
• Consequence: ARL14EP-DT ENST00000527819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310
• Publications: 6 publications found

Genes affected

ARL14EP-DT (HGNC:55517): (ARL14EP divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000527819.2. 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
	ARL14EP-DT	NR_187431.1		n.250+97608G>A		intron	N/A
	ARL14EP-DT	NR_187432.1		n.429+97608G>A		intron	N/A
	ARL14EP-DT	NR_187433.1		n.250+97608G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARL14EP-DT	ENST00000527819.2	TSL:3	n.471-62429G>A		intron	N/A
	ARL14EP-DT	ENST00000662729.1		n.293-62429G>A		intron	N/A
	ARL14EP-DT	ENST00000726808.1		n.517-62429G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72324 AN: 151852 Hom.: 17346 Cov.: 32

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.457

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.476 AC: 72362 AN: 151970 Hom.: 17351 Cov.: 32 AF XY: 0.482 AC XY: 35799 AN XY: 74280

African (AFR) AF: 0.533 AC: 22089 AN: 41430

American (AMR) AF: 0.438 AC: 6691 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1614 AN: 3466

East Asian (EAS) AF: 0.640 AC: 3301 AN: 5156

South Asian (SAS) AF: 0.554 AC: 2670 AN: 4822

European-Finnish (FIN) AF: 0.514 AC: 5437 AN: 10584

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29175 AN: 67938

Other (OTH) AF: 0.455 AC: 958 AN: 2106

Alfa AF: 0.447 Hom.: 7942

Bravo AF: 0.471

Asia WGS AF: 0.541 AC: 1880 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.4
DANN	Benign	0.60
PhyloP100		0.31

Splicing

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

dbSNP: rs518357;

hg19: chr11-30240829;