ENST00000527819.2:n.471-58144A>G

Variant names:

• chr11-30214997-T-C
• rs555621
• ENST00000527819.2:n.471-58144A>G

Variant summary

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

The ENST00000527819.2(ARL14EP-DT):​n.471-58144A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 152,016 control chromosomes in the GnomAD database, including 17,673 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 (17673 hom., cov: 32)
• Consequence: ARL14EP-DT ENST00000527819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.789
• Publications: 11 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARL14EP-DT	NR_187431.1	n.250+101893A>G		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187432.1	n.429+101893A>G		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187433.1	n.250+101893A>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARL14EP-DT	ENST00000527819.2	n.471-58144A>G		intron_variant	Intron 3 of 5	3
ARL14EP-DT	ENST00000662729.1	n.293-58144A>G		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726808.1	n.517-58144A>G		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726809.1	n.375-53949A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72464 AN: 151898 Hom.: 17656 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.477 AC: 72522 AN: 152016 Hom.: 17673 Cov.: 32 AF XY: 0.484 AC XY: 35948 AN XY: 74330

African (AFR) AF: 0.563 AC: 23341 AN: 41444

American (AMR) AF: 0.494 AC: 7547 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1521 AN: 3470

East Asian (EAS) AF: 0.672 AC: 3474 AN: 5168

South Asian (SAS) AF: 0.574 AC: 2759 AN: 4808

European-Finnish (FIN) AF: 0.490 AC: 5182 AN: 10574

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27341 AN: 67966

Other (OTH) AF: 0.454 AC: 960 AN: 2114

Alfa AF: 0.431 Hom.: 7187

Bravo AF: 0.482

Asia WGS AF: 0.569 AC: 1977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.27
DANN	Benign	0.48
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs555621; hg19: chr11-30236544;