rs832177

Variant names:

• chr1-201279072-G-A
• rs832177

Your query was ambiguous. Multiple possible variants found:

• chr1-201279072-G-A
• chr1-201279072-G-C

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 0.802 in 152,172 control chromosomes in the GnomAD database, including 49,912 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 0.80 (49912 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.802 AC: 122021 AN: 152054 Hom.: 49891 Cov.: 33

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.802 AC: 122074 AN: 152172 Hom.: 49912 Cov.: 33 AF XY: 0.803 AC XY: 59772 AN XY: 74392

African (AFR) AF: 0.638 AC: 26460 AN: 41476

American (AMR) AF: 0.845 AC: 12934 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 2581 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5168 AN: 5170

South Asian (SAS) AF: 0.903 AC: 4349 AN: 4818

European-Finnish (FIN) AF: 0.859 AC: 9100 AN: 10596

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.865 AC: 58857 AN: 68022

Other (OTH) AF: 0.800 AC: 1690 AN: 2112

Alfa AF: 0.835 Hom.: 30153

Bravo AF: 0.793

Asia WGS AF: 0.930 AC: 3234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.58
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs832177; hg19: chr1-201248200;