rs605765

Variant names:

• chr11-30195956-C-T
• rs605765
• ENST00000527819.2:n.471-39103G>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.471-39103G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 152,074 control chromosomes in the GnomAD database, including 33,649 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 0.66 (33649 hom., cov: 32)
• Consequence: ARL14EP-DT ENST00000527819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495
• Publications: 7 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.845 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+120934G>A		intron	N/A
	ARL14EP-DT	NR_187432.1		n.429+120934G>A		intron	N/A
	ARL14EP-DT	NR_187433.1		n.251-111556G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARL14EP-DT	ENST00000527819.2	TSL:3	n.471-39103G>A		intron	N/A
	ARL14EP-DT	ENST00000662729.1		n.293-39103G>A		intron	N/A
	ARL14EP-DT	ENST00000726808.1		n.517-39103G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100115 AN: 151956 Hom.: 33618 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.659 AC: 100195 AN: 152074 Hom.: 33649 Cov.: 32 AF XY: 0.662 AC XY: 49201 AN XY: 74334

African (AFR) AF: 0.777 AC: 32232 AN: 41470

American (AMR) AF: 0.552 AC: 8431 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2059 AN: 3470

East Asian (EAS) AF: 0.866 AC: 4489 AN: 5184

South Asian (SAS) AF: 0.660 AC: 3183 AN: 4826

European-Finnish (FIN) AF: 0.647 AC: 6840 AN: 10564

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40849 AN: 67972

Other (OTH) AF: 0.646 AC: 1364 AN: 2112

Alfa AF: 0.612 Hom.: 18115

Bravo AF: 0.654

Asia WGS AF: 0.746 AC: 2593 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.47
DANN	Benign	0.48
PhyloP100		-0.49

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: rs605765;

hg19: chr11-30217503;