rs1234302

Variant names:

• chr1-173152425-A-C
• rs1234302

Your query was ambiguous. Multiple possible variants found:

• chr1-173152425-A-C
• chr1-173152425-A-T

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 0.234 in 151,922 control chromosomes in the GnomAD database, including 4,467 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 0.23 (4467 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.277 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: 0.234 AC: 35520 AN: 151806 Hom.: 4469 Cov.: 31

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.0899

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.234 AC: 35513 AN: 151922 Hom.: 4467 Cov.: 31 AF XY: 0.227 AC XY: 16838 AN XY: 74244

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.0902

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.257

Alfa AF: 0.248 Hom.: 3223

Bravo AF: 0.232

Asia WGS AF: 0.188 AC: 656 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.7
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1234302; hg19: chr1-173121564;