1-215269100-C-G

Variant names:

• chr1-215269100-C-G
• rs4372225

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 0.778 in 152,100 control chromosomes in the GnomAD database, including 46,478 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 0.78 (46478 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 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: 0.778 AC: 118195 AN: 151982 Hom.: 46456 Cov.: 31

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.778 AC: 118267 AN: 152100 Hom.: 46478 Cov.: 31 AF XY: 0.785 AC XY: 58344 AN XY: 74352

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.813

Gnomad4 ASJ AF: 0.801

Gnomad4 EAS AF: 0.927

Gnomad4 SAS AF: 0.872

Gnomad4 FIN AF: 0.890

Gnomad4 NFE AF: 0.807

Gnomad4 OTH AF: 0.765

Alfa AF: 0.757 Hom.: 2425

Bravo AF: 0.764

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.40
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4372225; hg19: chr1-215442443;