chr11-30204981-G-A

Variant names:

• chr11-30204981-G-A
• rs11031006
• ENST00000527819.2:n.471-48128C>T

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000527819.2(ARL14EP-DT):​n.471-48128C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,116 control chromosomes in the GnomAD database, including 1,022 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 0.11 (1022 hom., cov: 32)
• Consequence: ARL14EP-DT ENST00000527819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.09
• Publications: 74 publications found

Genes affected

ARL14EP-DT (HGNC:55517): (ARL14EP divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.12).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARL14EP-DT	NR_187431.1	n.250+111909C>T		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187432.1	n.429+111909C>T		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187433.1	n.250+111909C>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.471-48128C>T		intron_variant	Intron 3 of 5	3
ARL14EP-DT	ENST00000662729.1	n.293-48128C>T		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726808.1	n.517-48128C>T		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726809.1	n.375-43933C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16619 AN: 151998 Hom.: 1019 Cov.: 32

Gnomad AFR AF: 0.0592

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0985

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0328

Gnomad SAS AF: 0.0984

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.109 AC: 16626 AN: 152116 Hom.: 1022 Cov.: 32 AF XY: 0.109 AC XY: 8110 AN XY: 74356

African (AFR) AF: 0.0591 AC: 2455 AN: 41514

American (AMR) AF: 0.0983 AC: 1502 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 414 AN: 3466

East Asian (EAS) AF: 0.0331 AC: 171 AN: 5166

South Asian (SAS) AF: 0.0991 AC: 477 AN: 4812

European-Finnish (FIN) AF: 0.168 AC: 1775 AN: 10580

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

European-Non Finnish (NFE) AF: 0.140 AC: 9489 AN: 67984

Other (OTH) AF: 0.105 AC: 221 AN: 2112

Alfa AF: 0.129 Hom.: 2333

Bravo AF: 0.102

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.12
CADD	Benign	22
DANN	Benign	0.69
PhyloP100		3.1

Splicing

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

Other links and lift over

dbSNP: rs11031006; hg19: chr11-30226528;