rs11031006

Positions:

• chr11-30204981-G-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000662729.1(ARL14EP-DT):​n.293-48128C>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 0.109 in 152,116 control chromosomes in the GnomAD database, including 1,022 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 0.11 (1022 hom., cov: 32)
• Consequence: ARL14EP-DT ENST00000662729.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.09

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.12).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARL14EP-DT	XR_007062639.1	n.351+111909C>T		intron_variant, non_coding_transcript_variant
ARL14EP-DT	XR_931152.3	n.530+111909C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARL14EP-DT	ENST00000662729.1	n.293-48128C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16619 AN: 151998 Hom.: 1019 Cov.: 32

Gnomad AFR AF: 0.0592

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0985

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0328

Gnomad SAS AF: 0.0984

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.109 AC: 16626 AN: 152116 Hom.: 1022 Cov.: 32 AF XY: 0.109 AC XY: 8110 AN XY: 74356

Gnomad4 AFR AF: 0.0591

Gnomad4 AMR AF: 0.0983

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.0331

Gnomad4 SAS AF: 0.0991

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.105

Alfa AF: 0.132 Hom.: 1956

Bravo AF: 0.102

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.12
CADD	Benign	22
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11031006; hg19: chr11-30226528;