rs1577879

chr1-80747260-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 0.191 in 151,314 control chromosomes in the GnomAD database, including 2,987 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 0.19 (2987 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 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: 0.191 AC: 28827 AN: 151196 Hom.: 2970 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.0858

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.191 AC: 28874 AN: 151314 Hom.: 2987 Cov.: 32 AF XY: 0.191 AC XY: 14124 AN XY: 73964

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.0858

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.190

Alfa AF: 0.190 Hom.: 3568

Bravo AF: 0.190

Asia WGS AF: 0.269 AC: 936 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.59
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1577879; hg19: chr1-81212945;