1-217425988-G-C

Variant names:

• chr1-217425988-G-C
• rs12128013

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 0.305 in 152,148 control chromosomes in the GnomAD database, including 7,327 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 0.30 (7327 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 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: 0.305 AC: 46332 AN: 152030 Hom.: 7325 Cov.: 33

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.0909

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.305 AC: 46347 AN: 152148 Hom.: 7327 Cov.: 33 AF XY: 0.299 AC XY: 22261 AN XY: 74374

African (AFR) AF: 0.355 AC: 14741 AN: 41486

American (AMR) AF: 0.242 AC: 3703 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1148 AN: 3468

East Asian (EAS) AF: 0.0909 AC: 471 AN: 5182

South Asian (SAS) AF: 0.297 AC: 1433 AN: 4824

European-Finnish (FIN) AF: 0.221 AC: 2345 AN: 10600

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.316 AC: 21486 AN: 67986

Other (OTH) AF: 0.334 AC: 707 AN: 2116

Alfa AF: 0.169 Hom.: 334

Bravo AF: 0.305

Asia WGS AF: 0.209 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.018
DANN	Benign	0.52
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs12128013; hg19: chr1-217599330;