6-28981429-G-C

Position:

• chr6-28981429-G-C

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 0.341 in 151,930 control chromosomes in the GnomAD database, including 10,197 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 0.34 (10197 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.535 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: 0.341 AC: 51696 AN: 151812 Hom.: 10176 Cov.: 32

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.341 AC: 51754 AN: 151930 Hom.: 10197 Cov.: 32 AF XY: 0.343 AC XY: 25493 AN XY: 74264

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.335

Alfa AF: 0.295 Hom.: 1027

Bravo AF: 0.350

Asia WGS AF: 0.282 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	0.50
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9257445; hg19: chr6-28949206;