rs1499384

Variant names:

• chr14-42579845-A-G
• rs1499384
• ENST00000557251.1:n.167-123260A>G

Variant summary

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

The ENST00000557251.1(ENSG00000258394):​n.167-123260A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0436 in 152,134 control chromosomes in the GnomAD database, including 170 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 0.044 (170 hom., cov: 32)
• Consequence: ENSG00000258394 ENST00000557251.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680
• Publications: 1 publications found

Genes affected

ENSG00000258394 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0554 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000557251.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258394	ENST00000557251.1	TSL:5	n.167-123260A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0436 AC: 6621 AN: 152016 Hom.: 169 Cov.: 32

Gnomad AFR AF: 0.0304

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0311

Gnomad ASJ AF: 0.0366

Gnomad EAS AF: 0.0154

Gnomad SAS AF: 0.0112

Gnomad FIN AF: 0.0586

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0569

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0436 AC: 6629 AN: 152134 Hom.: 170 Cov.: 32 AF XY: 0.0420 AC XY: 3123 AN XY: 74372

African (AFR) AF: 0.0306 AC: 1271 AN: 41558

American (AMR) AF: 0.0311 AC: 475 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0366 AC: 127 AN: 3468

East Asian (EAS) AF: 0.0155 AC: 80 AN: 5178

South Asian (SAS) AF: 0.0112 AC: 54 AN: 4826

European-Finnish (FIN) AF: 0.0586 AC: 621 AN: 10596

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0569 AC: 3866 AN: 67908

Other (OTH) AF: 0.0468 AC: 99 AN: 2114

Alfa AF: 0.0527 Hom.: 223

Bravo AF: 0.0405

Asia WGS AF: 0.0190 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.7
DANN	Benign	0.76
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs1499384; hg19: chr14-43049048;