rs12026758

Variant names:

• chr1-91672609-G-A
• rs12026758

Your query was ambiguous. Multiple possible variants found:

• chr1-91672609-G-A
• chr1-91672609-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 0.127 in 152,198 control chromosomes in the GnomAD database, including 2,460 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 0.13 (2460 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.669
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 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: 0.126 AC: 19195 AN: 152080 Hom.: 2445 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.0714

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.0903

Gnomad FIN AF: 0.0261

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0269

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.127 AC: 19257 AN: 152198 Hom.: 2460 Cov.: 32 AF XY: 0.129 AC XY: 9610 AN XY: 74408

African (AFR) AF: 0.259 AC: 10757 AN: 41494

American (AMR) AF: 0.180 AC: 2748 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0714 AC: 248 AN: 3472

East Asian (EAS) AF: 0.514 AC: 2649 AN: 5158

South Asian (SAS) AF: 0.0899 AC: 434 AN: 4826

European-Finnish (FIN) AF: 0.0261 AC: 277 AN: 10614

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0269 AC: 1831 AN: 68020

Other (OTH) AF: 0.129 AC: 274 AN: 2116

Alfa AF: 0.0712 Hom.: 2123

Bravo AF: 0.145

Asia WGS AF: 0.311 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.18
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs12026758; hg19: chr1-92138166;