6-130460539-A-G

Position:

• chr6-130460539-A-G

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 0.124 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.0824

Gnomad4 ASJ AF: 0.0620

Gnomad4 EAS AF: 0.0793

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.0903

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0670 Hom.: 99

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6928900; hg19: chr6-130781684;