rs11579504

Variant names:

• chr1-17306751-A-G
• rs11579504

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 0.224 in 152,044 control chromosomes in the GnomAD database, including 4,003 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 0.22 (4003 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.289 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: 0.224 AC: 34092 AN: 151926 Hom.: 3992 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.224 AC: 34133 AN: 152044 Hom.: 4003 Cov.: 32 AF XY: 0.225 AC XY: 16733 AN XY: 74314

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.236

Alfa AF: 0.214 Hom.: 324

Bravo AF: 0.228

Asia WGS AF: 0.228 AC: 796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.90
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11579504; hg19: chr1-17633246;