rs204999

Variant names:

• chr6-32142202-A-G
• rs204999

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 0.28 in 152,026 control chromosomes in the GnomAD database, including 6,487 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 (6487 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 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: 0.280 AC: 42552 AN: 151908 Hom.: 6486 Cov.: 31

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0959

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.280 AC: 42564 AN: 152026 Hom.: 6487 Cov.: 31 AF XY: 0.270 AC XY: 20030 AN XY: 74318

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.0965

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.277

Alfa AF: 0.268 Hom.: 8688

Bravo AF: 0.294

Asia WGS AF: 0.132 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs204999; hg19: chr6-32109979;