rs12092285

Variant names:

• chr1-177165573-G-A
• rs12092285

Your query was ambiguous. Multiple possible variants found:

• chr1-177165573-G-A
• chr1-177165573-G-T

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 0.271 in 151,998 control chromosomes in the GnomAD database, including 9,288 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 0.27 (9288 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.889
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41143 AN: 151880 Hom.: 9257 Cov.: 32

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0881

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.271 AC: 41217 AN: 151998 Hom.: 9288 Cov.: 32 AF XY: 0.265 AC XY: 19713 AN XY: 74300

African (AFR) AF: 0.625 AC: 25906 AN: 41424

American (AMR) AF: 0.197 AC: 3007 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 488 AN: 3472

East Asian (EAS) AF: 0.217 AC: 1117 AN: 5158

South Asian (SAS) AF: 0.128 AC: 616 AN: 4818

European-Finnish (FIN) AF: 0.0881 AC: 930 AN: 10558

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8343 AN: 67980

Other (OTH) AF: 0.225 AC: 475 AN: 2108

Alfa AF: 0.212 Hom.: 960

Bravo AF: 0.299

Asia WGS AF: 0.210 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.9
DANN	Benign	0.15
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs12092285; hg19: chr1-177134709;