rs601681

Variant names:

• chr11-30212847-C-T
• rs601681
• ENST00000527819.2:n.471-55994G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000527819.2(ARL14EP-DT):​n.471-55994G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151,860 control chromosomes in the GnomAD database, including 16,249 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 0.46 (16249 hom., cov: 32)
• Consequence: ARL14EP-DT ENST00000527819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000527819.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARL14EP-DT	NR_187431.1		n.250+104043G>A		intron	N/A
	ARL14EP-DT	NR_187432.1		n.429+104043G>A		intron	N/A
	ARL14EP-DT	NR_187433.1		n.250+104043G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARL14EP-DT	ENST00000527819.2	TSL:3	n.471-55994G>A		intron	N/A
	ARL14EP-DT	ENST00000662729.1		n.293-55994G>A		intron	N/A
	ARL14EP-DT	ENST00000726808.1		n.517-55994G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69667 AN: 151742 Hom.: 16243 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.459 AC: 69708 AN: 151860 Hom.: 16249 Cov.: 32 AF XY: 0.465 AC XY: 34486 AN XY: 74190

African (AFR) AF: 0.536 AC: 22206 AN: 41418

American (AMR) AF: 0.416 AC: 6344 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1515 AN: 3464

East Asian (EAS) AF: 0.640 AC: 3310 AN: 5170

South Asian (SAS) AF: 0.549 AC: 2638 AN: 4802

European-Finnish (FIN) AF: 0.492 AC: 5168 AN: 10500

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27202 AN: 67940

Other (OTH) AF: 0.439 AC: 928 AN: 2112

Alfa AF: 0.424 Hom.: 32750

Bravo AF: 0.455

Asia WGS AF: 0.537 AC: 1864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.67
DANN	Benign	0.81
PhyloP100		-2.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs601681;

hg19: chr11-30234394;