chr1-229740350-T-G

Variant names:

• chr1-229740350-T-G
• rs559272

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 0.263 in 151,766 control chromosomes in the GnomAD database, including 5,306 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 0.26 (5306 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39884 AN: 151648 Hom.: 5299 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.263 AC: 39916 AN: 151766 Hom.: 5306 Cov.: 32 AF XY: 0.260 AC XY: 19315 AN XY: 74200

African (AFR) AF: 0.293 AC: 12137 AN: 41410

American (AMR) AF: 0.266 AC: 4042 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1282 AN: 3466

East Asian (EAS) AF: 0.266 AC: 1375 AN: 5170

South Asian (SAS) AF: 0.280 AC: 1350 AN: 4816

European-Finnish (FIN) AF: 0.216 AC: 2288 AN: 10572

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16525 AN: 67824

Other (OTH) AF: 0.284 AC: 597 AN: 2100

Alfa AF: 0.234 Hom.: 550

Bravo AF: 0.268

Asia WGS AF: 0.281 AC: 975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.57
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs559272; hg19: chr1-229876097;