chr11-30212847-C-T

Position:

• chr11-30212847-C-T

Variant summary

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

The ENST00000662729.1(ARL14EP-DT):​n.293-55994G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151,860 control chromosomes in the GnomAD database, including 16,249 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 0.46 (16249 hom., cov: 32)
• Consequence: ARL14EP-DT ENST00000662729.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43

Genes affected

ARL14EP-DT (HGNC:55517): (ARL14EP divergent transcript)

ACMG classification

Verdict is Benign. Variant got -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 = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARL14EP-DT	XR_007062639.1	n.351+104043G>A		intron_variant, non_coding_transcript_variant
ARL14EP-DT	XR_931152.3	n.530+104043G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARL14EP-DT	ENST00000662729.1	n.293-55994G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69667 AN: 151742 Hom.: 16243 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.459 AC: 69708 AN: 151860 Hom.: 16249 Cov.: 32 AF XY: 0.465 AC XY: 34486 AN XY: 74190

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.439

Alfa AF: 0.414 Hom.: 19841

Bravo AF: 0.455

Asia WGS AF: 0.537 AC: 1864 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	0.67
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs601681; hg19: chr11-30234394;