rs9321244

chr6-130629904-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 0.0881 in 152,138 control chromosomes in the GnomAD database, including 886 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 0.088 (886 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.249 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: 0.0880 AC: 13379 AN: 152018 Hom.: 878 Cov.: 32

Gnomad AFR AF: 0.0371

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.0590

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.0932

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0768

Gnomad OTH AF: 0.0950

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

GnomAD4 genome AF: 0.0881 AC: 13408 AN: 152138 Hom.: 886 Cov.: 32 AF XY: 0.0943 AC XY: 7017 AN XY: 74388

Gnomad4 AFR AF: 0.0373

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.0590

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.0932

Gnomad4 NFE AF: 0.0768

Gnomad4 OTH AF: 0.0992

Alfa AF: 0.0873 Hom.: 80

Bravo AF: 0.0887

Asia WGS AF: 0.267 AC: 927 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.3
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9321244; hg19: chr6-130951049;