rs6034909

Variant names:

• chr20-1852009-A-G
• rs6034909

Your query was ambiguous. Multiple possible variants found:

• chr20-1852009-A-G
• chr20-1852009-A-T

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 0.239 in 152,146 control chromosomes in the GnomAD database, including 4,927 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 0.24 (4927 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.85

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 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: 0.239 AC: 36335 AN: 152026 Hom.: 4920 Cov.: 33

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.239 AC: 36377 AN: 152146 Hom.: 4927 Cov.: 33 AF XY: 0.237 AC XY: 17656 AN XY: 74386

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.262

Alfa AF: 0.194 Hom.: 6378

Bravo AF: 0.250

Asia WGS AF: 0.283 AC: 982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	5.3
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6034909; hg19: chr20-1832655;