chr11-30218631-C-A

Variant names:

• chr11-30218631-C-A
• rs11031010
• ENST00000527819.2:n.471-61778G>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.471-61778G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,240 control chromosomes in the GnomAD database, including 1,091 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 0.11 (1091 hom., cov: 32)
• Consequence: ARL14EP-DT ENST00000527819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54
• Publications: 19 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARL14EP-DT	NR_187431.1	n.250+98259G>T		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187432.1	n.429+98259G>T		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187433.1	n.250+98259G>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARL14EP-DT	ENST00000527819.2	n.471-61778G>T		intron_variant	Intron 3 of 5	3
ARL14EP-DT	ENST00000662729.1	n.293-61778G>T		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726808.1	n.517-61778G>T		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726809.1	n.375-57583G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17303 AN: 152122 Hom.: 1088 Cov.: 32

Gnomad AFR AF: 0.0627

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0336

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.114 AC: 17309 AN: 152240 Hom.: 1091 Cov.: 32 AF XY: 0.112 AC XY: 8335 AN XY: 74418

African (AFR) AF: 0.0626 AC: 2604 AN: 41570

American (AMR) AF: 0.125 AC: 1909 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3472

East Asian (EAS) AF: 0.0339 AC: 175 AN: 5162

South Asian (SAS) AF: 0.101 AC: 486 AN: 4826

European-Finnish (FIN) AF: 0.125 AC: 1326 AN: 10604

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 10019 AN: 68004

Other (OTH) AF: 0.115 AC: 242 AN: 2110

Alfa AF: 0.133 Hom.: 502

Bravo AF: 0.111

Asia WGS AF: 0.0630 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.078
DANN	Benign	0.68
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs11031010; hg19: chr11-30240178;