rs10835649

Positions:

• chr11-30307628-A-G

Variant summary

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

The ENST00000662729.1(ARL14EP-DT):​n.292+9262T>C 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 0.132 in 152,228 control chromosomes in the GnomAD database, including 1,382 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 0.13 (1382 hom., cov: 31)
• Consequence: ARL14EP-DT ENST00000662729.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARL14EP-DT	XR_007062639.1	n.351+9262T>C		intron_variant, non_coding_transcript_variant
ARL14EP-DT	XR_931152.3	n.530+9262T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARL14EP-DT	ENST00000662729.1	n.292+9262T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20039 AN: 152110 Hom.: 1378 Cov.: 31

Gnomad AFR AF: 0.0975

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0354

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.132 AC: 20059 AN: 152228 Hom.: 1382 Cov.: 31 AF XY: 0.132 AC XY: 9795 AN XY: 74434

Gnomad4 AFR AF: 0.0977

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.0356

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.125

Alfa AF: 0.131 Hom.: 227

Bravo AF: 0.127

Asia WGS AF: 0.0660 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.3
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: rs10835649; hg19: chr11-30329175;