11-30235575-A-G

Variant names:

• chr11-30235575-A-G
• rs560078
• ENST00000527819.2:n.471-78722T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000527819.2(ARL14EP-DT):​n.471-78722T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 152,048 control chromosomes in the GnomAD database, including 19,154 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 0.50 (19154 hom., cov: 32)
• Consequence: ARL14EP-DT ENST00000527819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200
• 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=-1.02).
• 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+81315T>C		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187432.1	n.429+81315T>C		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187433.1	n.250+81315T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARL14EP-DT	ENST00000527819.2	n.471-78722T>C		intron_variant	Intron 3 of 5	3
ARL14EP-DT	ENST00000662729.1	n.293-78722T>C		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726808.1	n.517-78722T>C		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726809.1	n.375-74527T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75712 AN: 151930 Hom.: 19137 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.498 AC: 75766 AN: 152048 Hom.: 19154 Cov.: 32 AF XY: 0.505 AC XY: 37526 AN XY: 74312

African (AFR) AF: 0.573 AC: 23756 AN: 41466

American (AMR) AF: 0.520 AC: 7940 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1623 AN: 3470

East Asian (EAS) AF: 0.673 AC: 3480 AN: 5168

South Asian (SAS) AF: 0.578 AC: 2784 AN: 4816

European-Finnish (FIN) AF: 0.514 AC: 5433 AN: 10566

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.431 AC: 29323 AN: 67984

Other (OTH) AF: 0.473 AC: 998 AN: 2108

Alfa AF: 0.324 Hom.: 832

Bravo AF: 0.502

Asia WGS AF: 0.575 AC: 1995 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.38
PhyloP100		0.020

Splicing

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

Other links and lift over

dbSNP: rs560078; hg19: chr11-30257122;