rs601640

Positions:

• chr11-30212885-G-A
• chr11-30212885-G-C
• chr11-30212885-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000662729.1(ARL14EP-DT):​n.293-56032C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,948 control chromosomes in the GnomAD database, including 17,400 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 0.47 (17400 hom., cov: 32)
• Consequence: ARL14EP-DT ENST00000662729.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARL14EP-DT	XR_007062639.1	n.351+104005C>T		intron_variant, non_coding_transcript_variant
ARL14EP-DT	XR_931152.3	n.530+104005C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARL14EP-DT	ENST00000662729.1	n.293-56032C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71959 AN: 151830 Hom.: 17389 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.474 AC: 72009 AN: 151948 Hom.: 17400 Cov.: 32 AF XY: 0.481 AC XY: 35686 AN XY: 74250

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.454

Alfa AF: 0.439 Hom.: 1849

Bravo AF: 0.478

Asia WGS AF: 0.566 AC: 1967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.65
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs601640; hg19: chr11-30234432;