chr1-26409282-A-G

Variant names:

• chr1-26409282-A-G
• rs12122703

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 0.438 in 151,402 control chromosomes in the GnomAD database, including 15,919 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 0.44 (15919 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66313 AN: 151286 Hom.: 15911 Cov.: 30

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.438 AC: 66342 AN: 151402 Hom.: 15919 Cov.: 30 AF XY: 0.437 AC XY: 32286 AN XY: 73940

African (AFR) AF: 0.261 AC: 10771 AN: 41318

American (AMR) AF: 0.471 AC: 7149 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1754 AN: 3452

East Asian (EAS) AF: 0.142 AC: 730 AN: 5154

South Asian (SAS) AF: 0.478 AC: 2294 AN: 4800

European-Finnish (FIN) AF: 0.507 AC: 5311 AN: 10468

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.544 AC: 36873 AN: 67728

Other (OTH) AF: 0.428 AC: 898 AN: 2100

Alfa AF: 0.517 Hom.: 27727

Bravo AF: 0.423

Asia WGS AF: 0.290 AC: 1011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.37
DANN	Benign	0.28
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs12122703; hg19: chr1-26735773;