6-28235522-A-G

Variant names:

• chr6-28235522-A-G
• rs9380069

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 0.127 in 152,198 control chromosomes in the GnomAD database, including 1,300 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 0.13 (1300 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 32 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.141 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: 0.127 AC: 19380 AN: 152080 Hom.: 1300 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0718

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0856

Gnomad FIN AF: 0.0777

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.127 AC: 19387 AN: 152198 Hom.: 1300 Cov.: 32 AF XY: 0.123 AC XY: 9154 AN XY: 74430

African (AFR) AF: 0.142 AC: 5912 AN: 41516

American (AMR) AF: 0.141 AC: 2157 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0718 AC: 249 AN: 3470

East Asian (EAS) AF: 0.149 AC: 773 AN: 5176

South Asian (SAS) AF: 0.0863 AC: 416 AN: 4822

European-Finnish (FIN) AF: 0.0777 AC: 824 AN: 10608

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8692 AN: 67998

Other (OTH) AF: 0.112 AC: 237 AN: 2114

Alfa AF: 0.128 Hom.: 4118

Bravo AF: 0.135

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.53
DANN	Benign	0.47
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9380069; hg19: chr6-28203300;