6-32750904-A-G

Position:

• chr6-32750904-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 0.617 in 151,950 control chromosomes in the GnomAD database, including 29,338 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 0.62 (29338 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32750904A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93626 AN: 151830 Hom.: 29301 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.617 AC: 93722 AN: 151950 Hom.: 29338 Cov.: 32 AF XY: 0.622 AC XY: 46214 AN XY: 74266

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.814

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.676

Alfa AF: 0.589 Hom.: 10166

Bravo AF: 0.630

Asia WGS AF: 0.725 AC: 2515 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.9
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9276490; hg19: chr6-32718681;