rs10835649

Variant names:

• chr11-30307628-A-G
• rs10835649
• ENST00000527819.2:n.470+9262T>C

Variant summary

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

The ENST00000527819.2(ARL14EP-DT):​n.470+9262T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,228 control chromosomes in the GnomAD database, including 1,382 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 0.13 (1382 hom., cov: 31)
• Consequence: ARL14EP-DT ENST00000527819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 10 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 (NFE) allele frequency at 95% confidence interval = 0.153 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+9262T>C		intron	N/A
	ARL14EP-DT	NR_187432.1		n.429+9262T>C		intron	N/A
	ARL14EP-DT	NR_187433.1		n.250+9262T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARL14EP-DT	ENST00000527819.2	TSL:3	n.470+9262T>C		intron	N/A
	ARL14EP-DT	ENST00000662729.1		n.292+9262T>C		intron	N/A
	ARL14EP-DT	ENST00000726808.1		n.516+9262T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20039 AN: 152110 Hom.: 1378 Cov.: 31

Gnomad AFR AF: 0.0975

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0354

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.132 AC: 20059 AN: 152228 Hom.: 1382 Cov.: 31 AF XY: 0.132 AC XY: 9795 AN XY: 74434

African (AFR) AF: 0.0977 AC: 4056 AN: 41522

American (AMR) AF: 0.134 AC: 2042 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3468

East Asian (EAS) AF: 0.0356 AC: 185 AN: 5190

South Asian (SAS) AF: 0.101 AC: 488 AN: 4828

European-Finnish (FIN) AF: 0.180 AC: 1907 AN: 10596

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10567 AN: 68014

Other (OTH) AF: 0.125 AC: 265 AN: 2112

Alfa AF: 0.131 Hom.: 228

Bravo AF: 0.127

Asia WGS AF: 0.0660 AC: 227 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	4.3
DANN	Benign	0.57
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs10835649; hg19: chr11-30329175;