11-30222321-G-T

Variant names:

• chr11-30222321-G-T
• rs1782507
• ENST00000527819.2:n.471-65468C>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.471-65468C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 151,986 control chromosomes in the GnomAD database, including 38,383 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 (38383 hom., cov: 32)
• Consequence: ARL14EP-DT ENST00000527819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293
• Publications: 12 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARL14EP-DT	NR_187431.1	n.250+94569C>A		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187432.1	n.429+94569C>A		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187433.1	n.250+94569C>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.471-65468C>A		intron_variant	Intron 3 of 5	3
ARL14EP-DT	ENST00000662729.1	n.293-65468C>A		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726808.1	n.517-65468C>A		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726809.1	n.375-61273C>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107353 AN: 151870 Hom.: 38350 Cov.: 32

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.707 AC: 107431 AN: 151986 Hom.: 38383 Cov.: 32 AF XY: 0.711 AC XY: 52836 AN XY: 74280

African (AFR) AF: 0.802 AC: 33302 AN: 41520

American (AMR) AF: 0.684 AC: 10424 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2162 AN: 3472

East Asian (EAS) AF: 0.905 AC: 4671 AN: 5162

South Asian (SAS) AF: 0.690 AC: 3320 AN: 4810

European-Finnish (FIN) AF: 0.686 AC: 7243 AN: 10558

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44062 AN: 67902

Other (OTH) AF: 0.690 AC: 1453 AN: 2106

Alfa AF: 0.671 Hom.: 107576

Bravo AF: 0.710

Asia WGS AF: 0.778 AC: 2705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.97
DANN	Benign	0.36
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1782507; hg19: chr11-30243868;