6-28175340-A-G

Variant names:

• chr6-28175340-A-G
• rs9380064

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 0.11 in 152,202 control chromosomes in the GnomAD database, including 1,037 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 0.11 (1037 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.569
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.14 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: 0.110 AC: 16710 AN: 152084 Hom.: 1035 Cov.: 32

Gnomad AFR AF: 0.0823

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0712

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.0769

Gnomad FIN AF: 0.0669

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.110 AC: 16717 AN: 152202 Hom.: 1037 Cov.: 32 AF XY: 0.105 AC XY: 7838 AN XY: 74428

African (AFR) AF: 0.0820 AC: 3406 AN: 41532

American (AMR) AF: 0.145 AC: 2218 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0712 AC: 247 AN: 3470

East Asian (EAS) AF: 0.115 AC: 596 AN: 5178

South Asian (SAS) AF: 0.0780 AC: 376 AN: 4820

European-Finnish (FIN) AF: 0.0669 AC: 710 AN: 10612

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8811 AN: 67988

Other (OTH) AF: 0.101 AC: 214 AN: 2114

Alfa AF: 0.125 Hom.: 4100

Bravo AF: 0.116

Asia WGS AF: 0.0940 AC: 328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.85
DANN	Benign	0.64
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs9380064; hg19: chr6-28143118;