1-226509828-C-G

Variant names:

• chr1-226509828-C-G
• rs1727029

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.327 in 151,910 control chromosomes in the GnomAD database, including 8,307 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 0.33 (8307 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193

ACMG classification

Verdict is Benign. Variant got -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 = 0.483 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: 0.327 AC: 49561 AN: 151790 Hom.: 8299 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.327 AC: 49625 AN: 151910 Hom.: 8307 Cov.: 32 AF XY: 0.330 AC XY: 24489 AN XY: 74260

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.337

Alfa AF: 0.307 Hom.: 917

Bravo AF: 0.326

Asia WGS AF: 0.482 AC: 1675 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	14
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1727029; hg19: chr1-226697529;