rs6519194

Variant names:

• chr22-39523519-G-A
• rs6519194

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 0.214 in 152,200 control chromosomes in the GnomAD database, including 3,940 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 0.21 (3940 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.264 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: 0.214 AC: 32596 AN: 152082 Hom.: 3942 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.0577

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.214 AC: 32596 AN: 152200 Hom.: 3940 Cov.: 33 AF XY: 0.215 AC XY: 15975 AN XY: 74400

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.0575

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.230

Alfa AF: 0.248 Hom.: 837

Bravo AF: 0.206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6519194; hg19: chr22-39919524;