6-415406-A-G

Position:

• chr6-415406-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 0.799 in 152,084 control chromosomes in the GnomAD database, including 48,933 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 0.80 (48933 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.77

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.415406A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121378 AN: 151966 Hom.: 48907 Cov.: 31

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.799 AC: 121459 AN: 152084 Hom.: 48933 Cov.: 31 AF XY: 0.799 AC XY: 59367 AN XY: 74338

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.816

Gnomad4 ASJ AF: 0.864

Gnomad4 EAS AF: 0.736

Gnomad4 SAS AF: 0.896

Gnomad4 FIN AF: 0.800

Gnomad4 NFE AF: 0.855

Gnomad4 OTH AF: 0.798

Alfa AF: 0.834 Hom.: 11538

Bravo AF: 0.791

Asia WGS AF: 0.790 AC: 2751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.53
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9503644; hg19: chr6-415406;