ENST00000527819.2:n.471-68376T>C

Variant names:

• chr11-30225229-A-G
• rs621686
• ENST00000527819.2:n.471-68376T>C

Variant summary

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

The ENST00000527819.2(ARL14EP-DT):​n.471-68376T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 151,978 control chromosomes in the GnomAD database, including 1,219 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 0.11 (1219 hom., cov: 31)
• Consequence: ARL14EP-DT ENST00000527819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 5 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARL14EP-DT	NR_187431.1	n.250+91661T>C		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187432.1	n.429+91661T>C		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187433.1	n.250+91661T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARL14EP-DT	ENST00000527819.2	n.471-68376T>C		intron_variant	Intron 3 of 5	3
ARL14EP-DT	ENST00000662729.1	n.293-68376T>C		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726808.1	n.517-68376T>C		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726809.1	n.375-64181T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17035 AN: 151860 Hom.: 1220 Cov.: 31

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0744

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.00309

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0928

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0751

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.112 AC: 17048 AN: 151978 Hom.: 1219 Cov.: 31 AF XY: 0.113 AC XY: 8363 AN XY: 74268

African (AFR) AF: 0.201 AC: 8318 AN: 41402

American (AMR) AF: 0.0743 AC: 1133 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 432 AN: 3472

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5174

South Asian (SAS) AF: 0.162 AC: 782 AN: 4824

European-Finnish (FIN) AF: 0.0928 AC: 980 AN: 10566

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0751 AC: 5105 AN: 67980

Other (OTH) AF: 0.109 AC: 229 AN: 2108

Alfa AF: 0.0944 Hom.: 533

Bravo AF: 0.112

Asia WGS AF: 0.0800 AC: 279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.66
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs621686; hg19: chr11-30246776;