chr20-33968971-G-A

Position:

• chr20-33968971-G-A

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 0.091 in 152,074 control chromosomes in the GnomAD database, including 1,155 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 0.091 (1155 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.740

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.372 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: 0.0908 AC: 13802 AN: 151954 Hom.: 1143 Cov.: 31

Gnomad AFR AF: 0.0600

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.0599

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.0814

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0557

Gnomad OTH AF: 0.0994

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

GnomAD4 genome AF: 0.0910 AC: 13834 AN: 152074 Hom.: 1155 Cov.: 31 AF XY: 0.0983 AC XY: 7308 AN XY: 74342

Gnomad4 AFR AF: 0.0606

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.0599

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.0814

Gnomad4 NFE AF: 0.0557

Gnomad4 OTH AF: 0.0970

Alfa AF: 0.0641 Hom.: 227

Bravo AF: 0.0995

Asia WGS AF: 0.267 AC: 928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.9
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6059594; hg19: chr20-32556777;