rs9389020

Positions:

• chr6-132641914-T-C
• chr6-132641914-T-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 0.255 in 152,032 control chromosomes in the GnomAD database, including 5,296 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 0.26 (5296 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.742

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38751 AN: 151914 Hom.: 5286 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.255 AC: 38784 AN: 152032 Hom.: 5296 Cov.: 32 AF XY: 0.259 AC XY: 19237 AN XY: 74306

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.233

Alfa AF: 0.276 Hom.: 12233

Bravo AF: 0.247

Asia WGS AF: 0.364 AC: 1263 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9389020; hg19: chr6-132963053;