rs1577879

Variant names:

• chr1-80747260-G-A
• rs1577879

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.137 AC: 5657 AN: 41360

American (AMR) AF: 0.260 AC: 3939 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.0858 AC: 297 AN: 3460

East Asian (EAS) AF: 0.305 AC: 1565 AN: 5138

South Asian (SAS) AF: 0.193 AC: 929 AN: 4804

European-Finnish (FIN) AF: 0.225 AC: 2364 AN: 10522

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.198 AC: 13401 AN: 67562

Other (OTH) AF: 0.190 AC: 397 AN: 2090

Alfa AF: 0.190 Hom.: 4240

Bravo AF: 0.190

Asia WGS AF: 0.269 AC: 936 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.75
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs1577879; hg19: chr1-81212945;