ENST00000527819.2:n.470+76469T>C

Variant names:

• chr11-30240421-A-G
• rs7951733
• ENST00000527819.2:n.470+76469T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000527819.2(ARL14EP-DT):​n.470+76469T>C variant causes a intron 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 ENST00000527819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 9 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ARL14EP-DT	NR_187431.1	n.250+76469T>C		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187432.1	n.429+76469T>C		intron_variant	Intron 3 of 3
ARL14EP-DT	NR_187433.1	n.250+76469T>C		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+76469T>C		intron_variant	Intron 3 of 5	3
ARL14EP-DT	ENST00000662729.1	n.292+76469T>C		intron_variant	Intron 3 of 4
ARL14EP-DT	ENST00000726808.1	n.516+76469T>C		intron_variant	Intron 3 of 4

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

African (AFR) AF: 0.0131 AC: 544 AN: 41562

American (AMR) AF: 0.0402 AC: 615 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0159 AC: 55 AN: 3470

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5186

South Asian (SAS) AF: 0.0104 AC: 50 AN: 4820

European-Finnish (FIN) AF: 0.0771 AC: 818 AN: 10614

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0720 AC: 4898 AN: 68022

Other (OTH) AF: 0.0360 AC: 76 AN: 2114

Alfa AF: 0.0559 Hom.: 353

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7951733; hg19: chr11-30261968;