rs560078

Variant names:

• chr11-30235575-A-C
• rs560078
• ENST00000527819.2:n.471-78722T>G

Your query was ambiguous. Multiple possible variants found:

• chr11-30235575-A-C
• chr11-30235575-A-G
• chr11-30235575-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000527819.2(ARL14EP-DT):​n.471-78722T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: ARL14EP-DT ENST00000527819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARL14EP-DT	NR_187431.1	n.250+81315T>G		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187432.1	n.429+81315T>G		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187433.1	n.250+81315T>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARL14EP-DT	ENST00000527819.2	n.471-78722T>G		intron_variant	Intron 3 of 5	3
ARL14EP-DT	ENST00000662729.1	n.293-78722T>G		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726808.1	n.517-78722T>G		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726809.1	n.375-74527T>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.37
PhyloP100		0.020

Splicing

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

Other links and lift over

dbSNP: rs560078; hg19: chr11-30257122;