chr11-30075383-A-C

Variant names:

• chr11-30075383-A-C
• rs665153
• ENST00000527819.2:n.624+8930T>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.624+8930T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 151,932 control chromosomes in the GnomAD database, including 39,543 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 0.71 (39543 hom., cov: 31)
• Consequence: ARL14EP-DT ENST00000527819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 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.251-30928T>G		intron	N/A
	ARL14EP-DT	NR_187432.1		n.430-30928T>G		intron	N/A
	ARL14EP-DT	NR_187433.1		n.338+8930T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARL14EP-DT	ENST00000527819.2	TSL:3	n.624+8930T>G		intron	N/A
	ARL14EP-DT	ENST00000662729.1		n.359-30928T>G		intron	N/A
	ARL14EP-DT	ENST00000669123.1		n.95-30928T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108255 AN: 151814 Hom.: 39541 Cov.: 31

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.713 AC: 108307 AN: 151932 Hom.: 39543 Cov.: 31 AF XY: 0.712 AC XY: 52844 AN XY: 74260

African (AFR) AF: 0.550 AC: 22774 AN: 41402

American (AMR) AF: 0.785 AC: 11973 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.865 AC: 3000 AN: 3468

East Asian (EAS) AF: 0.982 AC: 5067 AN: 5158

South Asian (SAS) AF: 0.754 AC: 3632 AN: 4820

European-Finnish (FIN) AF: 0.647 AC: 6830 AN: 10556

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52560 AN: 67972

Other (OTH) AF: 0.752 AC: 1583 AN: 2106

Alfa AF: 0.763 Hom.: 178279

Bravo AF: 0.720

Asia WGS AF: 0.844 AC: 2933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.49
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs665153; hg19: chr11-30096930;