11-30230805-G-T

Position:

• chr11-30230805-G-T

Variant summary

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

The NR_187431.1(ARL14EP-DT):​n.250+86085C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,196 control chromosomes in the GnomAD database, including 1,134 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.12 (1134 hom., cov: 33)
• Consequence: ARL14EP-DT NR_187431.1 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: 0.730

Genes affected

ARL14EP-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARL14EP-DT	NR_187431.1	n.250+86085C>A		intron_variant
ARL14EP-DT	NR_187432.1	n.429+86085C>A		intron_variant
ARL14EP-DT	NR_187433.1	n.250+86085C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARL14EP-DT	ENST00000662729.1	n.293-73952C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17665 AN: 152076 Hom.: 1131 Cov.: 33

Gnomad AFR AF: 0.0636

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0336

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.116 AC: 17671 AN: 152196 Hom.: 1134 Cov.: 33 AF XY: 0.114 AC XY: 8506 AN XY: 74406

Gnomad4 AFR AF: 0.0636

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.0338

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0655 Hom.: 74

Bravo AF: 0.113

Asia WGS AF: 0.0640 AC: 220 AN: 3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Hypogonadotropic hypogonadism 24 without anosmia Other:1

association, no assertion criteria provided

clinical testing

Gromoll Lab CeRA, University of Muenster

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	19
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10835638; hg19: chr11-30252352;