rs6568421

Variant names:

• chr6-105987150-A-G
• rs6568421

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 0.23 in 152,126 control chromosomes in the GnomAD database, including 4,402 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 0.23 (4402 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.285 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: 0.230 AC: 34961 AN: 152008 Hom.: 4397 Cov.: 31

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.230 AC: 34978 AN: 152126 Hom.: 4402 Cov.: 31 AF XY: 0.225 AC XY: 16754 AN XY: 74378

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.00231

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.241

Alfa AF: 0.269 Hom.: 7077

Bravo AF: 0.223

Asia WGS AF: 0.0820 AC: 291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	11
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6568421; hg19: chr6-106435025;