11-30220778-C-T

Variant names:

• chr11-30220778-C-T
• rs572883
• ENST00000527819.2:n.471-63925G>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.471-63925G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,934 control chromosomes in the GnomAD database, including 18,648 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 (18648 hom., cov: 33)
• Consequence: ARL14EP-DT ENST00000527819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.953
• Publications: 4 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 = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARL14EP-DT	NR_187431.1	n.250+96112G>A		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187432.1	n.429+96112G>A		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187433.1	n.250+96112G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARL14EP-DT	ENST00000527819.2	n.471-63925G>A		intron_variant	Intron 3 of 5	3
ARL14EP-DT	ENST00000662729.1	n.293-63925G>A		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726808.1	n.517-63925G>A		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726809.1	n.375-59730G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74802 AN: 151816 Hom.: 18636 Cov.: 33

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.493 AC: 74851 AN: 151934 Hom.: 18648 Cov.: 33 AF XY: 0.500 AC XY: 37088 AN XY: 74242

African (AFR) AF: 0.555 AC: 22982 AN: 41430

American (AMR) AF: 0.516 AC: 7865 AN: 15244

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

East Asian (EAS) AF: 0.673 AC: 3482 AN: 5172

South Asian (SAS) AF: 0.570 AC: 2742 AN: 4812

European-Finnish (FIN) AF: 0.515 AC: 5425 AN: 10532

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

European-Non Finnish (NFE) AF: 0.431 AC: 29320 AN: 67962

Other (OTH) AF: 0.470 AC: 989 AN: 2106

Alfa AF: 0.464 Hom.: 2041

Bravo AF: 0.495

Asia WGS AF: 0.570 AC: 1978 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.026
DANN	Benign	0.41
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs572883; hg19: chr11-30242325;