rs708491

Variant names:

• chr14-52298226-A-G
• rs708491

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 0.236 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.00830

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.291

Alfa AF: 0.284 Hom.: 8511

Bravo AF: 0.233

Asia WGS AF: 0.0890 AC: 310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs708491; hg19: chr14-52764944;