rs1499384

chr14-42579845-A-G

Variant summary

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

The ENST00000557251.1(ENSG00000258394):n.167-123260A>G 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 0.0436 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: ENST00000557251.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

Genes affected

(HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.0554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000557251.1	n.167-123260A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.0306

Gnomad4 AMR AF: 0.0311

Gnomad4 ASJ AF: 0.0366

Gnomad4 EAS AF: 0.0155

Gnomad4 SAS AF: 0.0112

Gnomad4 FIN AF: 0.0586

Gnomad4 NFE AF: 0.0569

Gnomad4 OTH AF: 0.0468

Alfa AF: 0.0522 Hom.: 162

Bravo AF: 0.0405

Asia WGS AF: 0.0190 AC: 67 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	3.7
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1499384; hg19: chr14-43049048;