rs11031002

Positions:

• chr11-30193714-T-A

Variant summary

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

The ENST00000662729.1(ARL14EP-DT):​n.293-36861A>T 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 0.0997 in 152,020 control chromosomes in the GnomAD database, including 834 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 0.10 (834 hom., cov: 32)
• Consequence: ARL14EP-DT ENST00000662729.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARL14EP-DT	XR_007062639.1	n.351+123176A>T		intron_variant, non_coding_transcript_variant
ARL14EP-DT	XR_931152.3	n.530+123176A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARL14EP-DT	ENST00000662729.1	n.293-36861A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0997 AC: 15150 AN: 151902 Hom.: 831 Cov.: 32

Gnomad AFR AF: 0.0580

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0932

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0330

Gnomad SAS AF: 0.0980

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0997 AC: 15156 AN: 152020 Hom.: 834 Cov.: 32 AF XY: 0.0977 AC XY: 7258 AN XY: 74302

Gnomad4 AFR AF: 0.0579

Gnomad4 AMR AF: 0.0931

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0332

Gnomad4 SAS AF: 0.0987

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0559 Hom.: 55

Bravo AF: 0.0969

Asia WGS AF: 0.0600 AC: 206 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.034
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11031002; hg19: chr11-30215261;