rs601640

Variant names:

• chr11-30212885-G-A
• rs601640
• ENST00000527819.2:n.471-56032C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-30212885-G-A
• chr11-30212885-G-C
• chr11-30212885-G-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.471-56032C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,948 control chromosomes in the GnomAD database, including 17,400 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 0.47 (17400 hom., cov: 32)
• Consequence: ARL14EP-DT ENST00000527819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349
• Publications: 5 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 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+104005C>T		intron	N/A
	ARL14EP-DT	NR_187432.1		n.429+104005C>T		intron	N/A
	ARL14EP-DT	NR_187433.1		n.250+104005C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARL14EP-DT	ENST00000527819.2	TSL:3	n.471-56032C>T		intron	N/A
	ARL14EP-DT	ENST00000662729.1		n.293-56032C>T		intron	N/A
	ARL14EP-DT	ENST00000726808.1		n.517-56032C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71959 AN: 151830 Hom.: 17389 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.474 AC: 72009 AN: 151948 Hom.: 17400 Cov.: 32 AF XY: 0.481 AC XY: 35686 AN XY: 74250

African (AFR) AF: 0.553 AC: 22899 AN: 41424

American (AMR) AF: 0.494 AC: 7539 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1516 AN: 3464

East Asian (EAS) AF: 0.673 AC: 3479 AN: 5172

South Asian (SAS) AF: 0.565 AC: 2722 AN: 4818

European-Finnish (FIN) AF: 0.491 AC: 5165 AN: 10530

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

European-Non Finnish (NFE) AF: 0.402 AC: 27335 AN: 67952

Other (OTH) AF: 0.454 AC: 957 AN: 2110

Alfa AF: 0.439 Hom.: 1849

Bravo AF: 0.478

Asia WGS AF: 0.566 AC: 1967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.65
DANN	Benign	0.43
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs601640; hg19: chr11-30234432;