chr14-52298226-A-G

Variant names:

• chr14-52298226-A-G
• rs708491
• ENST00000726797.1:n.299+14610T>C

Variant summary

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

The ENST00000726797.1(ENSG00000289424):​n.299+14610T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,208 control chromosomes in the GnomAD database, including 4,693 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 0.24 (4693 hom., cov: 33)
• Consequence: ENSG00000289424 ENST00000726797.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 4 publications found

Genes affected

ENSG00000289424 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726797.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289424	ENST00000726797.1		n.299+14610T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35866 AN: 152090 Hom.: 4695 Cov.: 33

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.00828

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.236 AC: 35870 AN: 152208 Hom.: 4693 Cov.: 33 AF XY: 0.231 AC XY: 17220 AN XY: 74424

African (AFR) AF: 0.162 AC: 6722 AN: 41530

American (AMR) AF: 0.229 AC: 3509 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1079 AN: 3472

East Asian (EAS) AF: 0.00830 AC: 43 AN: 5180

South Asian (SAS) AF: 0.144 AC: 693 AN: 4822

European-Finnish (FIN) AF: 0.266 AC: 2813 AN: 10590

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20161 AN: 68002

Other (OTH) AF: 0.291 AC: 615 AN: 2112

Alfa AF: 0.277 Hom.: 11455

Bravo AF: 0.233

Asia WGS AF: 0.0890 AC: 310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.98
DANN	Benign	0.56
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs708491; hg19: chr14-52764944;