chr6-32431509-A-G

Position:

• chr6-32431509-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 0.0927 in 152,244 control chromosomes in the GnomAD database, including 813 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 0.093 (813 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.825

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32431509A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0926 AC: 14091 AN: 152126 Hom.: 812 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.0546

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.0240

Gnomad SAS AF: 0.0660

Gnomad FIN AF: 0.0474

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0731

Gnomad OTH AF: 0.0900

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

GnomAD4 genome AF: 0.0927 AC: 14119 AN: 152244 Hom.: 813 Cov.: 32 AF XY: 0.0900 AC XY: 6700 AN XY: 74438

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.0546

Gnomad4 ASJ AF: 0.0775

Gnomad4 EAS AF: 0.0243

Gnomad4 SAS AF: 0.0655

Gnomad4 FIN AF: 0.0474

Gnomad4 NFE AF: 0.0731

Gnomad4 OTH AF: 0.0909

Alfa AF: 0.0804 Hom.: 239

Bravo AF: 0.0971

Asia WGS AF: 0.0590 AC: 205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.2
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9501624; hg19: chr6-32399286;