rs621686

Positions:

• chr11-30225229-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.293-68376T>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 0.112 in 151,978 control chromosomes in the GnomAD database, including 1,219 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 (1219 hom., cov: 31)
• Consequence: ARL14EP-DT ENST00000662729.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARL14EP-DT	XR_007062639.1	n.351+91661T>C		intron_variant, non_coding_transcript_variant
ARL14EP-DT	XR_931152.3	n.530+91661T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARL14EP-DT	ENST00000662729.1	n.293-68376T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17035 AN: 151860 Hom.: 1220 Cov.: 31

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0744

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.00309

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0928

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0751

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.112 AC: 17048 AN: 151978 Hom.: 1219 Cov.: 31 AF XY: 0.113 AC XY: 8363 AN XY: 74268

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.0743

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.0928

Gnomad4 NFE AF: 0.0751

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0941 Hom.: 478

Bravo AF: 0.112

Asia WGS AF: 0.0800 AC: 279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs621686; hg19: chr11-30246776;