6-32773229-T-C

Position:

• chr6-32773229-T-C

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 0.698 in 151,996 control chromosomes in the GnomAD database, including 37,090 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 0.70 (37090 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32773229T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.698 AC: 105990 AN: 151878 Hom.: 37075 Cov.: 32

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.698 AC: 106050 AN: 151996 Hom.: 37090 Cov.: 32 AF XY: 0.703 AC XY: 52198 AN XY: 74296

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.733

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.791

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.698

Alfa AF: 0.692 Hom.: 6566

Bravo AF: 0.687

Asia WGS AF: 0.753 AC: 2617 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2621419; hg19: chr6-32741006;