rs6864839

Positions:

• chr5-174643623-G-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 0.271 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;