chr11-30228630-C-T

Variant names:

• chr11-30228630-C-T
• rs1716022
• ENST00000527819.2:n.471-71777G>A

Variant summary

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

Score: -12 - Benign

-12

BP4_StrongBA1

The ENST00000527819.2(ARL14EP-DT):​n.471-71777G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,928 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: -2.81
• 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=-0.9).
• 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+88260G>A		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187432.1	n.429+88260G>A		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187433.1	n.250+88260G>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.471-71777G>A		intron_variant	Intron 3 of 5	3
ARL14EP-DT	ENST00000662729.1	n.293-71777G>A		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726808.1	n.517-71777G>A		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726809.1	n.375-67582G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74768 AN: 151810 Hom.: 18621 Cov.: 31

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.492 AC: 74817 AN: 151928 Hom.: 18633 Cov.: 31 AF XY: 0.499 AC XY: 37076 AN XY: 74238

African (AFR) AF: 0.553 AC: 22921 AN: 41416

American (AMR) AF: 0.519 AC: 7920 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1617 AN: 3472

East Asian (EAS) AF: 0.673 AC: 3476 AN: 5164

South Asian (SAS) AF: 0.570 AC: 2736 AN: 4804

European-Finnish (FIN) AF: 0.514 AC: 5431 AN: 10556

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

European-Non Finnish (NFE) AF: 0.431 AC: 29294 AN: 67946

Other (OTH) AF: 0.470 AC: 993 AN: 2112

Alfa AF: 0.470 Hom.: 5760

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	-0.90
CADD	Benign	0.19
DANN	Benign	0.42
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs1716022; hg19: chr11-30250177;