rs599957

Variant names:

• chr6-168704664-A-C
• rs599957

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 0.919 in 152,234 control chromosomes in the GnomAD database, including 64,307 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 0.92 (64307 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 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: 0.919 AC: 139820 AN: 152116 Hom.: 64277 Cov.: 32

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.908

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.953

Gnomad FIN AF: 0.920

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.919 AC: 139907 AN: 152234 Hom.: 64307 Cov.: 32 AF XY: 0.918 AC XY: 68349 AN XY: 74424

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.908

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.961

Gnomad4 SAS AF: 0.951

Gnomad4 FIN AF: 0.920

Gnomad4 NFE AF: 0.913

Gnomad4 OTH AF: 0.931

Alfa AF: 0.916 Hom.: 33935

Bravo AF: 0.919

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs599957; hg19: chr6-169104792;