6-833579-A-G

Position:

• chr6-833579-A-G

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 0.255 in 152,098 control chromosomes in the GnomAD database, including 5,474 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 0.26 (5474 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.381 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: 0.255 AC: 38776 AN: 151980 Hom.: 5463 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.255 AC: 38827 AN: 152098 Hom.: 5474 Cov.: 32 AF XY: 0.256 AC XY: 19034 AN XY: 74360

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.244

Alfa AF: 0.212 Hom.: 5848

Bravo AF: 0.260

Asia WGS AF: 0.298 AC: 1032 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2317222; hg19: chr6-833579;