6-28858628-A-G

Variant names:

• chr6-28858628-A-G
• rs176461

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 0.0556 in 152,242 control chromosomes in the GnomAD database, including 258 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 0.056 (258 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.941

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0755 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: 0.0556 AC: 8457 AN: 152124 Hom.: 257 Cov.: 32

Gnomad AFR AF: 0.0752

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.0409

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.0196

Gnomad SAS AF: 0.0823

Gnomad FIN AF: 0.0420

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0503

Gnomad OTH AF: 0.0621

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

GnomAD4 genome AF: 0.0556 AC: 8464 AN: 152242 Hom.: 258 Cov.: 32 AF XY: 0.0559 AC XY: 4158 AN XY: 74438

Gnomad4 AFR AF: 0.0752

Gnomad4 AMR AF: 0.0408

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.0197

Gnomad4 SAS AF: 0.0821

Gnomad4 FIN AF: 0.0420

Gnomad4 NFE AF: 0.0503

Gnomad4 OTH AF: 0.0615

Alfa AF: 0.0506 Hom.: 126

Bravo AF: 0.0563

Asia WGS AF: 0.0500 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.4
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: rs176461; hg19: chr6-28826405;