chr14-52300623-G-A

Variant names:

• chr14-52300623-G-A
• rs708494
• ENST00000726797.1:n.299+12213C>T

Variant summary

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

The ENST00000726797.1(ENSG00000289424):​n.299+12213C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 151,918 control chromosomes in the GnomAD database, including 20,140 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

• Frequency: Genomes: 𝑓 0.47 (20140 hom., cov: 31)
• Consequence: ENSG00000289424 ENST00000726797.1 intron
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: 0.164
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.646 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289424	ENST00000726797.1		n.299+12213C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71834 AN: 151800 Hom.: 20152 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.473 AC: 71805 AN: 151918 Hom.: 20140 Cov.: 31 AF XY: 0.464 AC XY: 34444 AN XY: 74236

African (AFR) AF: 0.197 AC: 8147 AN: 41408

American (AMR) AF: 0.442 AC: 6750 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2118 AN: 3466

East Asian (EAS) AF: 0.247 AC: 1274 AN: 5168

South Asian (SAS) AF: 0.307 AC: 1478 AN: 4814

European-Finnish (FIN) AF: 0.571 AC: 6010 AN: 10534

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.652 AC: 44273 AN: 67952

Other (OTH) AF: 0.515 AC: 1086 AN: 2110

Alfa AF: 0.577 Hom.: 47120

Bravo AF: 0.454

Asia WGS AF: 0.278 AC: 968 AN: 3478

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Asthma, aspirin-induced, susceptibility to Other:1

Dec 15, 2004

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.67
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs708494; hg19: chr14-52767341;