rs8008858

Variant names:

• chr14-54912497-T-A
• rs8008858

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;