ENST00000527819.2:n.470+79448C>T

Variant names:

• chr11-30237442-G-A
• rs615577
• ENST00000527819.2:n.470+79448C>T

Variant summary

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

The ENST00000527819.2(ARL14EP-DT):​n.470+79448C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 152,006 control chromosomes in the GnomAD database, including 18,631 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 0.49 (18631 hom., cov: 32)
• Consequence: ARL14EP-DT ENST00000527819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.412
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARL14EP-DT	NR_187431.1		n.250+79448C>T		intron	N/A
	ARL14EP-DT	NR_187432.1		n.429+79448C>T		intron	N/A
	ARL14EP-DT	NR_187433.1		n.250+79448C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARL14EP-DT	ENST00000527819.2	TSL:3	n.470+79448C>T		intron	N/A
	ARL14EP-DT	ENST00000662729.1		n.292+79448C>T		intron	N/A
	ARL14EP-DT	ENST00000726808.1		n.516+79448C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74784 AN: 151888 Hom.: 18619 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.492 AC: 74833 AN: 152006 Hom.: 18631 Cov.: 32 AF XY: 0.499 AC XY: 37087 AN XY: 74286

African (AFR) AF: 0.553 AC: 22931 AN: 41440

American (AMR) AF: 0.519 AC: 7920 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1623 AN: 3472

East Asian (EAS) AF: 0.672 AC: 3466 AN: 5154

South Asian (SAS) AF: 0.569 AC: 2743 AN: 4820

European-Finnish (FIN) AF: 0.515 AC: 5434 AN: 10556

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

European-Non Finnish (NFE) AF: 0.431 AC: 29299 AN: 67976

Other (OTH) AF: 0.468 AC: 988 AN: 2112

Alfa AF: 0.455 Hom.: 20710

Bravo AF: 0.496

Asia WGS AF: 0.570 AC: 1981 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.45
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs615577; hg19: chr11-30258989;