rs573179

Variant names:

• chr6-27881898-C-A
• rs573179

Your query was ambiguous. Multiple possible variants found:

• chr6-27881898-C-A
• chr6-27881898-C-T

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 0.266 in 150,962 control chromosomes in the GnomAD database, including 6,296 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 0.27 (6296 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.427 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: 0.265 AC: 40025 AN: 150900 Hom.: 6272 Cov.: 29

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.266 AC: 40083 AN: 150962 Hom.: 6296 Cov.: 29 AF XY: 0.260 AC XY: 19169 AN XY: 73678

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.245

Alfa AF: 0.198 Hom.: 2684

Bravo AF: 0.279

Asia WGS AF: 0.213 AC: 743 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs573179; hg19: chr6-27849676;