rs9321334

chr6-132245939-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 0.355 in 152,040 control chromosomes in the GnomAD database, including 11,387 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 0.36 (11387 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 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: 0.355 AC: 53963 AN: 151922 Hom.: 11349 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.355 AC: 54046 AN: 152040 Hom.: 11387 Cov.: 32 AF XY: 0.352 AC XY: 26132 AN XY: 74338

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.328

Alfa AF: 0.284 Hom.: 13574

Bravo AF: 0.361

Asia WGS AF: 0.371 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	5.4
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9321334; hg19: chr6-132567078; COSMIC: COSV69426558;