6-28843040-C-T

Position:

• chr6-28843040-C-T

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 0.377 in 151,914 control chromosomes in the GnomAD database, including 10,948 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 0.38 (10948 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 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: 0.377 AC: 57204 AN: 151796 Hom.: 10949 Cov.: 31

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.377 AC: 57225 AN: 151914 Hom.: 10948 Cov.: 31 AF XY: 0.377 AC XY: 27967 AN XY: 74226

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.362

Alfa AF: 0.368 Hom.: 6523

Bravo AF: 0.383

Asia WGS AF: 0.440 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs422331; hg19: chr6-28810817;