20-32855130-A-G

Position:

• chr20-32855130-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.026 in 152,282 control chromosomes in the GnomAD database, including 71 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 0.026 (71 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.026 (3956/152282) while in subpopulation NFE AF= 0.0399 (2711/68024). AF 95% confidence interval is 0.0386. There are 71 homozygotes in gnomad4. There are 1901 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 71 gene

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: 0.0260 AC: 3960 AN: 152164 Hom.: 71 Cov.: 32

Gnomad AFR AF: 0.00654

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0204

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.00352

Gnomad FIN AF: 0.0446

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0399

Gnomad OTH AF: 0.0225

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

GnomAD4 genome AF: 0.0260 AC: 3956 AN: 152282 Hom.: 71 Cov.: 32 AF XY: 0.0255 AC XY: 1901 AN XY: 74460

Gnomad4 AFR AF: 0.00652

Gnomad4 AMR AF: 0.0204

Gnomad4 ASJ AF: 0.0294

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.00353

Gnomad4 FIN AF: 0.0446

Gnomad4 NFE AF: 0.0399

Gnomad4 OTH AF: 0.0223

Alfa AF: 0.0341 Hom.: 14

Bravo AF: 0.0229

Asia WGS AF: 0.00115 AC: 5 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.5
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17297652; hg19: chr20-31442936;