6-32146738-A-T

Variant names:

• chr6-32146738-A-T
• rs9296009

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 0.205 in 152,076 control chromosomes in the GnomAD database, including 3,331 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 0.20 (3331 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31140 AN: 151958 Hom.: 3329 Cov.: 31

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.205 AC: 31167 AN: 152076 Hom.: 3331 Cov.: 31 AF XY: 0.207 AC XY: 15373 AN XY: 74330

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.152

Alfa AF: 0.198 Hom.: 405

Bravo AF: 0.204

Asia WGS AF: 0.128 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.8
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9296009; hg19: chr6-32114515;