chr1-80445429-G-A

Variant names:

• chr1-80445429-G-A
• rs12118390

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 0.0497 in 152,114 control chromosomes in the GnomAD database, including 419 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 0.050 (419 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.967
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 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: 0.0496 AC: 7543 AN: 151996 Hom.: 419 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.0226

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.0219

Gnomad SAS AF: 0.0131

Gnomad FIN AF: 0.0157

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0111

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0497 AC: 7559 AN: 152114 Hom.: 419 Cov.: 32 AF XY: 0.0489 AC XY: 3639 AN XY: 74368

African (AFR) AF: 0.142 AC: 5898 AN: 41506

American (AMR) AF: 0.0225 AC: 343 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0112 AC: 39 AN: 3472

East Asian (EAS) AF: 0.0219 AC: 113 AN: 5156

South Asian (SAS) AF: 0.0131 AC: 63 AN: 4820

European-Finnish (FIN) AF: 0.0157 AC: 167 AN: 10616

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0111 AC: 757 AN: 67978

Other (OTH) AF: 0.0374 AC: 79 AN: 2110

Alfa AF: 0.0289 Hom.: 475

Bravo AF: 0.0549

Asia WGS AF: 0.0200 AC: 68 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.50
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs12118390; hg19: chr1-80911114;