11-30195956-C-T

Position:

• chr11-30195956-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.293-39103G>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 0.659 in 152,074 control chromosomes in the GnomAD database, including 33,649 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 0.66 (33649 hom., cov: 32)
• Consequence: ARL14EP-DT ENST00000662729.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARL14EP-DT	XR_007062639.1	n.351+120934G>A		intron_variant, non_coding_transcript_variant
ARL14EP-DT	XR_931152.3	n.530+120934G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARL14EP-DT	ENST00000662729.1	n.293-39103G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100115 AN: 151956 Hom.: 33618 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.659 AC: 100195 AN: 152074 Hom.: 33649 Cov.: 32 AF XY: 0.662 AC XY: 49201 AN XY: 74334

Gnomad4 AFR AF: 0.777

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.660

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.646

Alfa AF: 0.612 Hom.: 16695

Bravo AF: 0.654

Asia WGS AF: 0.746 AC: 2593 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.47
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs605765; hg19: chr11-30217503;