rs439121

Positions:

• chr6-33225090-A-C
• chr6-33225090-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 0.276 in 152,102 control chromosomes in the GnomAD database, including 6,355 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 0.28 (6355 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41941 AN: 151984 Hom.: 6331 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.276 AC: 42004 AN: 152102 Hom.: 6355 Cov.: 32 AF XY: 0.280 AC XY: 20817 AN XY: 74364

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.290

Alfa AF: 0.276 Hom.: 7679

Bravo AF: 0.267

Asia WGS AF: 0.415 AC: 1440 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.7
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs439121; hg19: chr6-33192867;