rs665153

Positions:

• chr11-30075383-A-C
• chr11-30075383-A-G
• chr11-30075383-A-T

Variant summary

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

The ENST00000662729.1(ARL14EP-DT):​n.359-30928T>G 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 0.713 in 151,932 control chromosomes in the GnomAD database, including 39,543 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 0.71 (39543 hom., cov: 31)
• Consequence: ARL14EP-DT ENST00000662729.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARL14EP-DT	XR_007062639.1	n.352-30928T>G		intron_variant, non_coding_transcript_variant
ARL14EP-DT	XR_931152.3	n.531-30928T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARL14EP-DT	ENST00000662729.1	n.359-30928T>G		intron_variant, non_coding_transcript_variant
ARL14EP-DT	ENST00000527819.1	n.31+8930T>G		intron_variant, non_coding_transcript_variant		3
ARL14EP-DT	ENST00000669123.1	n.95-30928T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108255 AN: 151814 Hom.: 39541 Cov.: 31

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.713 AC: 108307 AN: 151932 Hom.: 39543 Cov.: 31 AF XY: 0.712 AC XY: 52844 AN XY: 74260

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.865

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.752

Alfa AF: 0.775 Hom.: 90933

Bravo AF: 0.720

Asia WGS AF: 0.844 AC: 2933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs665153; hg19: chr11-30096930;