rs590833

Variant names:

• chr11-30219485-G-A
• rs590833
• ENST00000527819.2:n.471-62632C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-30219485-G-A
• chr11-30219485-G-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.471-62632C>T 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 151,894 control chromosomes in the GnomAD database, including 18,633 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 (18633 hom., cov: 31)
• Consequence: ARL14EP-DT ENST00000527819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARL14EP-DT	NR_187431.1	n.250+97405C>T		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187432.1	n.429+97405C>T		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187433.1	n.250+97405C>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.471-62632C>T		intron_variant	Intron 3 of 5	3
ARL14EP-DT	ENST00000662729.1	n.293-62632C>T		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726808.1	n.517-62632C>T		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726809.1	n.375-58437C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74769 AN: 151776 Hom.: 18622 Cov.: 31

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: 0.569

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.493 AC: 74821 AN: 151894 Hom.: 18633 Cov.: 31 AF XY: 0.499 AC XY: 37064 AN XY: 74218

African (AFR) AF: 0.555 AC: 22975 AN: 41410

American (AMR) AF: 0.516 AC: 7876 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1619 AN: 3472

East Asian (EAS) AF: 0.673 AC: 3465 AN: 5148

South Asian (SAS) AF: 0.568 AC: 2733 AN: 4808

European-Finnish (FIN) AF: 0.515 AC: 5418 AN: 10528

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

European-Non Finnish (NFE) AF: 0.431 AC: 29321 AN: 67970

Other (OTH) AF: 0.468 AC: 985 AN: 2104

Alfa AF: 0.433 Hom.: 7106

Bravo AF: 0.496

Asia WGS AF: 0.571 AC: 1983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.61
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs590833; hg19: chr11-30241032;