11-30312676-C-T

Position:

• chr11-30312676-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+4214G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 151,756 control chromosomes in the GnomAD database, including 9,527 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 0.34 (9527 hom., cov: 32)
• Consequence: ARL14EP-DT NR_187431.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.914

Genes affected

ARL14EP-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARL14EP-DT	NR_187431.1	n.250+4214G>A		intron_variant
ARL14EP-DT	NR_187432.1	n.429+4214G>A		intron_variant
ARL14EP-DT	NR_187433.1	n.250+4214G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARL14EP-DT	ENST00000662729.1	n.292+4214G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52115 AN: 151638 Hom.: 9528 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.344 AC: 52135 AN: 151756 Hom.: 9527 Cov.: 32 AF XY: 0.350 AC XY: 25957 AN XY: 74158

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.323

Alfa AF: 0.284 Hom.: 12799

Bravo AF: 0.343

Asia WGS AF: 0.478 AC: 1661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.44
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1856142; hg19: chr11-30334223;