rs1856142

Variant names:

• chr11-30312676-C-A
• rs1856142
• ENST00000527819.2:n.470+4214G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-30312676-C-A
• chr11-30312676-C-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.470+4214G>T 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: -0.914
• Publications: 15 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=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARL14EP-DT	NR_187431.1	n.250+4214G>T		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187432.1	n.429+4214G>T		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187433.1	n.250+4214G>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.470+4214G>T		intron_variant	Intron 3 of 5	3
ARL14EP-DT	ENST00000662729.1	n.292+4214G>T		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726808.1	n.516+4214G>T		intron_variant	Intron 3 of 4

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

Alfa AF: 0.00 Hom.: 29089

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.33
DANN	Benign	0.53
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs1856142; hg19: chr11-30334223;