rs11031002

Variant names:

• chr11-30193714-T-A
• rs11031002
• ENST00000527819.2:n.471-36861A>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.471-36861A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0997 in 152,020 control chromosomes in the GnomAD database, including 834 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 0.10 (834 hom., cov: 32)
• Consequence: ARL14EP-DT ENST00000527819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 23 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 (NFE) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARL14EP-DT	NR_187431.1	n.250+123176A>T		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187432.1	n.429+123176A>T		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187433.1	n.251-109314A>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARL14EP-DT	ENST00000527819.2	n.471-36861A>T		intron_variant	Intron 3 of 5	3
ARL14EP-DT	ENST00000662729.1	n.293-36861A>T		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726808.1	n.517-36861A>T		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726809.1	n.375-32666A>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0997 AC: 15150 AN: 151902 Hom.: 831 Cov.: 32

Gnomad AFR AF: 0.0580

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0932

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0330

Gnomad SAS AF: 0.0980

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0997 AC: 15156 AN: 152020 Hom.: 834 Cov.: 32 AF XY: 0.0977 AC XY: 7258 AN XY: 74302

African (AFR) AF: 0.0579 AC: 2407 AN: 41538

American (AMR) AF: 0.0931 AC: 1418 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 357 AN: 3466

East Asian (EAS) AF: 0.0332 AC: 172 AN: 5176

South Asian (SAS) AF: 0.0987 AC: 474 AN: 4802

European-Finnish (FIN) AF: 0.111 AC: 1169 AN: 10564

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8825 AN: 67928

Other (OTH) AF: 0.101 AC: 212 AN: 2106

Alfa AF: 0.0559 Hom.: 55

Bravo AF: 0.0969

Asia WGS AF: 0.0600 AC: 206 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.034
DANN	Benign	0.39
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs11031002; hg19: chr11-30215261;