rs519007

Positions:

• chr6-108703637-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 0.291 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;