6-128820358-C-G

Variant names:

• chr6-128820358-C-G
• rs6928495

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.56 in 151,946 control chromosomes in the GnomAD database, including 24,197 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 0.56 (24197 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85004 AN: 151828 Hom.: 24193 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.560 AC: 85042 AN: 151946 Hom.: 24197 Cov.: 32 AF XY: 0.563 AC XY: 41809 AN XY: 74274

African (AFR) AF: 0.501 AC: 20748 AN: 41438

American (AMR) AF: 0.625 AC: 9531 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1788 AN: 3468

East Asian (EAS) AF: 0.807 AC: 4155 AN: 5146

South Asian (SAS) AF: 0.544 AC: 2619 AN: 4810

European-Finnish (FIN) AF: 0.591 AC: 6239 AN: 10564

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38131 AN: 67952

Other (OTH) AF: 0.557 AC: 1172 AN: 2106

Alfa AF: 0.434 Hom.: 1251

Bravo AF: 0.563

Asia WGS AF: 0.652 AC: 2268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.77
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs6928495; hg19: chr6-129141503;