rs708494

Positions:

• chr14-52300623-G-A
• chr14-52300623-G-C

Variant summary

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

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: Unknown
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: 0.164

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.515

Alfa AF: 0.590 Hom.: 6974

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

risk factor, no assertion criteria provided

literature only

OMIM

Dec 15, 2004

- -

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs708494; hg19: chr14-52767341;