rs9349112

Variant names:

• chr6-39290021-C-A
• rs9349112

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 0.27 in 152,066 control chromosomes in the GnomAD database, including 5,667 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 0.27 (5667 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 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: 0.270 AC: 40960 AN: 151948 Hom.: 5660 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.270 AC: 41004 AN: 152066 Hom.: 5667 Cov.: 32 AF XY: 0.273 AC XY: 20314 AN XY: 74312

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.266

Alfa AF: 0.255 Hom.: 1002

Bravo AF: 0.274

Asia WGS AF: 0.326 AC: 1137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	13
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: rs9349112; hg19: chr6-39257797;