rs519007

Variant names:

• chr6-108703637-G-A
• rs519007

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 0.291 in 144,276 control chromosomes in the GnomAD database, including 7,180 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 0.29 (7180 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 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: 0.291 AC: 41941 AN: 144176 Hom.: 7176 Cov.: 32

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.291 AC: 41985 AN: 144276 Hom.: 7180 Cov.: 32 AF XY: 0.296 AC XY: 20864 AN XY: 70530

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.251

Alfa AF: 0.291 Hom.: 1022

Bravo AF: 0.272

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.2
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs519007; hg19: chr6-109024840;