11-30154159-C-T

Variant names:

• chr11-30154159-C-T
• rs2226016
• ENST00000527819.2:n.536+2629G>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.536+2629G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,006 control chromosomes in the GnomAD database, including 8,163 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 0.32 (8163 hom., cov: 31)
• Consequence: ARL14EP-DT ENST00000527819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96
• 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=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.346 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.251-109704G>A		intron	N/A
	ARL14EP-DT	NR_187432.1		n.430-109704G>A		intron	N/A
	ARL14EP-DT	NR_187433.1		n.251-69759G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARL14EP-DT	ENST00000527819.2	TSL:3	n.536+2629G>A		intron	N/A
	ARL14EP-DT	ENST00000662729.1		n.358+2629G>A		intron	N/A
	ARL14EP-DT	ENST00000669123.1		n.94+2629G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48353 AN: 150892 Hom.: 8157 Cov.: 31

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.320 AC: 48380 AN: 151006 Hom.: 8163 Cov.: 31 AF XY: 0.322 AC XY: 23758 AN XY: 73696

African (AFR) AF: 0.278 AC: 11335 AN: 40726

American (AMR) AF: 0.277 AC: 4210 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 874 AN: 3466

East Asian (EAS) AF: 0.261 AC: 1338 AN: 5128

South Asian (SAS) AF: 0.257 AC: 1232 AN: 4788

European-Finnish (FIN) AF: 0.429 AC: 4492 AN: 10462

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23735 AN: 67900

Other (OTH) AF: 0.315 AC: 663 AN: 2104

Alfa AF: 0.325 Hom.: 1926

Bravo AF: 0.307

Asia WGS AF: 0.276 AC: 960 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	0.39
DANN	Benign	0.12
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs2226016; hg19: chr11-30175706;