rs439121

Variant names:

• chr6-33225090-A-C
• rs439121

Your query was ambiguous. Multiple possible variants found:

• chr6-33225090-A-C
• chr6-33225090-A-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.254 AC: 10558 AN: 41488

American (AMR) AF: 0.218 AC: 3329 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 951 AN: 3472

East Asian (EAS) AF: 0.631 AC: 3266 AN: 5176

South Asian (SAS) AF: 0.348 AC: 1679 AN: 4828

European-Finnish (FIN) AF: 0.327 AC: 3456 AN: 10560

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17946 AN: 67974

Other (OTH) AF: 0.290 AC: 613 AN: 2112

Alfa AF: 0.273 Hom.: 19313

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
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs439121; hg19: chr6-33192867;