chr11-30240421-A-G

Position:

• chr11-30240421-A-G

Variant summary

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

The ENST00000662729.1(ARL14EP-DT):​n.292+76469T>C 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 0.0467 in 152,282 control chromosomes in the GnomAD database, including 241 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 0.047 (241 hom., cov: 31)
• Consequence: ARL14EP-DT ENST00000662729.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARL14EP-DT	XR_007062639.1	n.351+76469T>C		intron_variant, non_coding_transcript_variant
ARL14EP-DT	XR_931152.3	n.530+76469T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARL14EP-DT	ENST00000662729.1	n.292+76469T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0468 AC: 7114 AN: 152164 Hom.: 241 Cov.: 31

Gnomad AFR AF: 0.0131

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0403

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0102

Gnomad FIN AF: 0.0771

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0720

Gnomad OTH AF: 0.0363

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

GnomAD4 genome AF: 0.0467 AC: 7114 AN: 152282 Hom.: 241 Cov.: 31 AF XY: 0.0449 AC XY: 3346 AN XY: 74456

Gnomad4 AFR AF: 0.0131

Gnomad4 AMR AF: 0.0402

Gnomad4 ASJ AF: 0.0159

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0104

Gnomad4 FIN AF: 0.0771

Gnomad4 NFE AF: 0.0720

Gnomad4 OTH AF: 0.0360

Alfa AF: 0.0629 Hom.: 139

Bravo AF: 0.0439

Asia WGS AF: 0.00664 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.8
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7951733; hg19: chr11-30261968;