rs6864839

Variant names:

• chr5-174643623-G-A
• rs6864839

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 0.271 in 151,496 control chromosomes in the GnomAD database, including 5,839 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 0.27 (5839 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.752

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.311 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: 0.271 AC: 41067 AN: 151378 Hom.: 5838 Cov.: 29

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.271 AC: 41082 AN: 151496 Hom.: 5839 Cov.: 29 AF XY: 0.273 AC XY: 20185 AN XY: 73964

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.291

Alfa AF: 0.300 Hom.: 901

Bravo AF: 0.260

Asia WGS AF: 0.289 AC: 1006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6864839; hg19: chr5-174070626;