21-34199605-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 0.0525 in 151,244 control chromosomes in the GnomAD database, including 332 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 0.052 (332 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0524 AC: 7926 AN: 151132 Hom.: 329 Cov.: 30

Gnomad AFR AF: 0.0160

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0383

Gnomad ASJ AF: 0.0912

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0893

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0525

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0525 AC: 7939 AN: 151244 Hom.: 332 Cov.: 30 AF XY: 0.0550 AC XY: 4063 AN XY: 73812

Gnomad4 AFR AF: 0.0160

Gnomad4 AMR AF: 0.0383

Gnomad4 ASJ AF: 0.0912

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.0893

Gnomad4 NFE AF: 0.0525

Gnomad4 OTH AF: 0.0578

Alfa AF: 0.0504 Hom.: 196

Bravo AF: 0.0465

Asia WGS AF: 0.185 AC: 643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.93
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8131349; hg19: chr21-35571906;