11-30230078-C-T

Variant names:

• chr11-30230078-C-T
• rs639403
• ENST00000527819.2:n.471-73225G>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.471-73225G>A 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 152,004 control chromosomes in the GnomAD database, including 18,641 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 (18641 hom., cov: 32)
• Consequence: ARL14EP-DT ENST00000527819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397
• Publications: 7 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 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+86812G>A		intron	N/A
	ARL14EP-DT	NR_187432.1		n.429+86812G>A		intron	N/A
	ARL14EP-DT	NR_187433.1		n.250+86812G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARL14EP-DT	ENST00000527819.2	TSL:3	n.471-73225G>A		intron	N/A
	ARL14EP-DT	ENST00000662729.1		n.293-73225G>A		intron	N/A
	ARL14EP-DT	ENST00000726808.1		n.517-73225G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74795 AN: 151886 Hom.: 18629 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.492 AC: 74844 AN: 152004 Hom.: 18641 Cov.: 32 AF XY: 0.499 AC XY: 37087 AN XY: 74294

African (AFR) AF: 0.554 AC: 22948 AN: 41452

American (AMR) AF: 0.518 AC: 7908 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1617 AN: 3470

East Asian (EAS) AF: 0.672 AC: 3471 AN: 5164

South Asian (SAS) AF: 0.569 AC: 2743 AN: 4822

European-Finnish (FIN) AF: 0.514 AC: 5429 AN: 10552

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

European-Non Finnish (NFE) AF: 0.431 AC: 29310 AN: 67970

Other (OTH) AF: 0.469 AC: 989 AN: 2110

Alfa AF: 0.456 Hom.: 21217

Bravo AF: 0.495

Asia WGS AF: 0.571 AC: 1983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.30
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs639403; hg19: chr11-30251625;