chr11-30217923-G-A

Variant names:

• chr11-30217923-G-A
• rs618611
• ENST00000527819.2:n.471-61070C>T

Variant summary

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

The ENST00000527819.2(ARL14EP-DT):​n.471-61070C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,966 control chromosomes in the GnomAD database, including 17,406 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 0.48 (17406 hom., cov: 32)
• Consequence: ARL14EP-DT ENST00000527819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.623 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARL14EP-DT	NR_187431.1		n.250+98967C>T		intron	N/A
	ARL14EP-DT	NR_187432.1		n.429+98967C>T		intron	N/A
	ARL14EP-DT	NR_187433.1		n.250+98967C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARL14EP-DT	ENST00000527819.2	TSL:3	n.471-61070C>T		intron	N/A
	ARL14EP-DT	ENST00000662729.1		n.293-61070C>T		intron	N/A
	ARL14EP-DT	ENST00000726808.1		n.517-61070C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72346 AN: 151848 Hom.: 17400 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.476 AC: 72389 AN: 151966 Hom.: 17406 Cov.: 32 AF XY: 0.482 AC XY: 35802 AN XY: 74254

African (AFR) AF: 0.541 AC: 22414 AN: 41440

American (AMR) AF: 0.434 AC: 6623 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1611 AN: 3466

East Asian (EAS) AF: 0.641 AC: 3310 AN: 5162

South Asian (SAS) AF: 0.555 AC: 2674 AN: 4820

European-Finnish (FIN) AF: 0.510 AC: 5384 AN: 10548

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 28983 AN: 67942

Other (OTH) AF: 0.455 AC: 961 AN: 2114

Alfa AF: 0.337 Hom.: 969

Bravo AF: 0.472

Asia WGS AF: 0.542 AC: 1882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.49
PhyloP100		0.044

Splicing

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

Other links and lift over

dbSNP: rs618611; hg19: chr11-30239470;