rs6888304

Variant names:

• chr5-31020414-A-G
• rs6888304

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 0.291 in 152,100 control chromosomes in the GnomAD database, including 6,737 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 0.29 (6737 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.572

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 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: 0.291 AC: 44182 AN: 151982 Hom.: 6729 Cov.: 33

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.291 AC: 44215 AN: 152100 Hom.: 6737 Cov.: 33 AF XY: 0.287 AC XY: 21353 AN XY: 74354

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.244

Alfa AF: 0.280 Hom.: 5385

Bravo AF: 0.286

Asia WGS AF: 0.181 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6888304; hg19: chr5-31020521;