1-12164239-TC-TCC

Variant names:

• chr1-12164239-T-TC
• rs35752907

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.029 (67 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507
• Publications: 1 publications found

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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: 0.0293 AC: 4310 AN: 146854 Hom.: 65 Cov.: 31

Gnomad AFR AF: 0.0190

Gnomad AMI AF: 0.0364

Gnomad AMR AF: 0.0196

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.0144

Gnomad SAS AF: 0.0187

Gnomad FIN AF: 0.0165

Gnomad MID AF: 0.00323

Gnomad NFE AF: 0.0411

Gnomad OTH AF: 0.0271

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0295 AC: 4332 AN: 146960 Hom.: 67 Cov.: 31 AF XY: 0.0272 AC XY: 1944 AN XY: 71578

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0195 AC: 774 AN: 39752

American (AMR) AF: 0.0195 AC: 287 AN: 14716

Ashkenazi Jewish (ASJ) AF: 0.0378 AC: 129 AN: 3416

East Asian (EAS) AF: 0.0144 AC: 72 AN: 5002

South Asian (SAS) AF: 0.0185 AC: 86 AN: 4640

European-Finnish (FIN) AF: 0.0165 AC: 163 AN: 9874

Middle Eastern (MID) AF: 0.00347 AC: 1 AN: 288

European-Non Finnish (NFE) AF: 0.0411 AC: 2729 AN: 66386

Other (OTH) AF: 0.0294 AC: 59 AN: 2008

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00556 Hom.: 2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs35752907; hg19: chr1-12224296;