1-79707126-G-A

Variant names:

• chr1-79707126-G-A
• rs12144807

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 0.174 in 151,722 control chromosomes in the GnomAD database, including 2,839 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 0.17 (2839 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26439 AN: 151606 Hom.: 2839 Cov.: 30

Gnomad AFR AF: 0.0703

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.174 AC: 26435 AN: 151722 Hom.: 2839 Cov.: 30 AF XY: 0.183 AC XY: 13551 AN XY: 74126

African (AFR) AF: 0.0701 AC: 2906 AN: 41446

American (AMR) AF: 0.270 AC: 4113 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 641 AN: 3462

East Asian (EAS) AF: 0.226 AC: 1169 AN: 5178

South Asian (SAS) AF: 0.140 AC: 675 AN: 4814

European-Finnish (FIN) AF: 0.338 AC: 3545 AN: 10474

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12781 AN: 67804

Other (OTH) AF: 0.157 AC: 330 AN: 2108

Alfa AF: 0.190 Hom.: 1642

Bravo AF: 0.171

Asia WGS AF: 0.156 AC: 543 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.55
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs12144807; hg19: chr1-80172811;