1-223512092-G-A

Position:

• chr1-223512092-G-A

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 0.373 in 151,670 control chromosomes in the GnomAD database, including 11,846 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 0.37 (11846 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.669

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56604 AN: 151552 Hom.: 11861 Cov.: 29

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.373 AC: 56602 AN: 151670 Hom.: 11846 Cov.: 29 AF XY: 0.375 AC XY: 27762 AN XY: 74124

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.400

Alfa AF: 0.410 Hom.: 1688

Bravo AF: 0.369

Asia WGS AF: 0.439 AC: 1528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.65
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12119648; hg19: chr1-223685434;