rs11579848

chr1-207955510-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 0.276 in 152,162 control chromosomes in the GnomAD database, including 6,328 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 0.28 (6328 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.819

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41991 AN: 152044 Hom.: 6326 Cov.: 33

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.0385

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.276 AC: 41995 AN: 152162 Hom.: 6328 Cov.: 33 AF XY: 0.266 AC XY: 19803 AN XY: 74394

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.0386

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.281

Alfa AF: 0.328 Hom.: 14200

Bravo AF: 0.274

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	12
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11579848; hg19: chr1-208128855;