chr14-55828862-G-A

Variant names:

• chr14-55828862-G-A
• rs1953358
• ENST00000729158.1:n.491+651G>A

Variant summary

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

The ENST00000729158.1(ENSG00000259868):​n.491+651G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 152,044 control chromosomes in the GnomAD database, including 16,904 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 (16904 hom., cov: 33)
• Consequence: ENSG00000259868 ENST00000729158.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389
• Publications: 5 publications found

Genes affected

ENSG00000259868 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729158.1. 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
	ENSG00000259868	ENST00000729158.1		n.491+651G>A		intron	N/A
	ENSG00000259868	ENST00000729159.1		n.386+25158G>A		intron	N/A
	ENSG00000259868	ENST00000729160.1		n.386+25158G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70812 AN: 151926 Hom.: 16886 Cov.: 33

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.466 AC: 70861 AN: 152044 Hom.: 16904 Cov.: 33 AF XY: 0.465 AC XY: 34545 AN XY: 74294

African (AFR) AF: 0.400 AC: 16598 AN: 41452

American (AMR) AF: 0.485 AC: 7411 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1865 AN: 3472

East Asian (EAS) AF: 0.662 AC: 3416 AN: 5160

South Asian (SAS) AF: 0.496 AC: 2392 AN: 4826

European-Finnish (FIN) AF: 0.421 AC: 4453 AN: 10574

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33044 AN: 67962

Other (OTH) AF: 0.458 AC: 965 AN: 2106

Alfa AF: 0.487 Hom.: 54528

Bravo AF: 0.472

Asia WGS AF: 0.537 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.60
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs1953358; hg19: chr14-56295580;