rs12722875

Variant names:

• chr1-116272862-T-A
• rs12722875

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 0.274 in 152,128 control chromosomes in the GnomAD database, including 5,959 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 0.27 (5959 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421

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 (SAS) allele frequency at 95% confidence interval = 0.335 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: 0.274 AC: 41648 AN: 152012 Hom.: 5953 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.274 AC: 41669 AN: 152128 Hom.: 5959 Cov.: 32 AF XY: 0.273 AC XY: 20315 AN XY: 74374

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.294

Alfa AF: 0.292 Hom.: 836

Bravo AF: 0.266

Asia WGS AF: 0.276 AC: 957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12722875; hg19: chr1-116815484;