ENST00000527819.2:n.470+4214G>A

Variant names:

• chr11-30312676-C-T
• rs1856142
• ENST00000527819.2:n.470+4214G>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.470+4214G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 151,756 control chromosomes in the GnomAD database, including 9,527 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 0.34 (9527 hom., cov: 32)
• Consequence: ARL14EP-DT ENST00000527819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.914
• Publications: 15 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 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+4214G>A		intron	N/A
	ARL14EP-DT	NR_187432.1		n.429+4214G>A		intron	N/A
	ARL14EP-DT	NR_187433.1		n.250+4214G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARL14EP-DT	ENST00000527819.2	TSL:3	n.470+4214G>A		intron	N/A
	ARL14EP-DT	ENST00000662729.1		n.292+4214G>A		intron	N/A
	ARL14EP-DT	ENST00000726808.1		n.516+4214G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52115 AN: 151638 Hom.: 9528 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.344 AC: 52135 AN: 151756 Hom.: 9527 Cov.: 32 AF XY: 0.350 AC XY: 25957 AN XY: 74158

African (AFR) AF: 0.435 AC: 18012 AN: 41404

American (AMR) AF: 0.302 AC: 4598 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1186 AN: 3464

East Asian (EAS) AF: 0.607 AC: 3141 AN: 5176

South Asian (SAS) AF: 0.456 AC: 2189 AN: 4804

European-Finnish (FIN) AF: 0.335 AC: 3529 AN: 10548

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18511 AN: 67836

Other (OTH) AF: 0.323 AC: 679 AN: 2104

Alfa AF: 0.294 Hom.: 29089

Bravo AF: 0.343

Asia WGS AF: 0.478 AC: 1661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.44
DANN	Benign	0.53
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs1856142; hg19: chr11-30334223;