rs8008858

chr14-54912497-T-A

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 0.305 in 151,966 control chromosomes in the GnomAD database, including 9,589 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 0.30 (9589 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46212 AN: 151848 Hom.: 9556 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.305 AC: 46317 AN: 151966 Hom.: 9589 Cov.: 32 AF XY: 0.303 AC XY: 22528 AN XY: 74286

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.275

Alfa AF: 0.252 Hom.: 871

Bravo AF: 0.319

Asia WGS AF: 0.196 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	5.4
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8008858; hg19: chr14-55379215;