rs1716022

Positions:

• chr11-30228630-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_187431.1(ARL14EP-DT):​n.250+88260G>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 NR_187431.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.81

Genes affected

ARL14EP-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ARL14EP-DT	NR_187431.1	n.250+88260G>A		intron_variant
ARL14EP-DT	NR_187432.1	n.429+88260G>A		intron_variant
ARL14EP-DT	NR_187433.1	n.250+88260G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARL14EP-DT	ENST00000662729.1	n.293-71777G>A		intron_variant

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

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.470

Alfa AF: 0.458 Hom.: 2680

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1716022; hg19: chr11-30250177;