6-130460539-A-G

Variant names:

• chr6-130460539-A-G
• rs6928900

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 0.124 in 152,210 control chromosomes in the GnomAD database, including 1,380 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 0.12 (1380 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 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: 0.124 AC: 18885 AN: 152092 Hom.: 1367 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0825

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.0794

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0903

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.124 AC: 18944 AN: 152210 Hom.: 1380 Cov.: 32 AF XY: 0.125 AC XY: 9274 AN XY: 74422

African (AFR) AF: 0.209 AC: 8690 AN: 41514

American (AMR) AF: 0.0824 AC: 1260 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0620 AC: 215 AN: 3470

East Asian (EAS) AF: 0.0793 AC: 411 AN: 5180

South Asian (SAS) AF: 0.147 AC: 706 AN: 4816

European-Finnish (FIN) AF: 0.112 AC: 1193 AN: 10610

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0903 AC: 6138 AN: 68010

Other (OTH) AF: 0.120 AC: 253 AN: 2114

Alfa AF: 0.0704 Hom.: 120

Bravo AF: 0.124

Asia WGS AF: 0.157 AC: 546 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.97
DANN	Benign	0.24
PhyloP100		0.027

Splicing

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

Other links and lift over

dbSNP: rs6928900; hg19: chr6-130781684;