chr11-30219282-C-T

Position:

• chr11-30219282-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+97608G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,970 control chromosomes in the GnomAD database, including 17,351 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 0.48 (17351 hom., cov: 32)
• Consequence: ARL14EP-DT NR_187431.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310

Genes affected

ARL14EP-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARL14EP-DT	NR_187431.1	n.250+97608G>A		intron_variant
ARL14EP-DT	NR_187432.1	n.429+97608G>A		intron_variant
ARL14EP-DT	NR_187433.1	n.250+97608G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARL14EP-DT	ENST00000662729.1	n.293-62429G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72324 AN: 151852 Hom.: 17346 Cov.: 32

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.476 AC: 72362 AN: 151970 Hom.: 17351 Cov.: 32 AF XY: 0.482 AC XY: 35799 AN XY: 74280

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.455

Alfa AF: 0.448 Hom.: 7196

Bravo AF: 0.471

Asia WGS AF: 0.541 AC: 1880 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.4
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs518357; hg19: chr11-30240829;