12-56805570-C-T

Variant names:

• chr12-56805570-C-T
• rs1870673

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 0.157 in 152,206 control chromosomes in the GnomAD database, including 2,595 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 0.16 (2595 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23866 AN: 152088 Hom.: 2594 Cov.: 32

Gnomad AFR AF: 0.0445

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0842

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.157 AC: 23857 AN: 152206 Hom.: 2595 Cov.: 32 AF XY: 0.150 AC XY: 11158 AN XY: 74432

African (AFR) AF: 0.0444 AC: 1847 AN: 41566

American (AMR) AF: 0.158 AC: 2410 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 975 AN: 3464

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5172

South Asian (SAS) AF: 0.0839 AC: 405 AN: 4828

European-Finnish (FIN) AF: 0.136 AC: 1442 AN: 10592

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16149 AN: 67982

Other (OTH) AF: 0.192 AC: 405 AN: 2110

Alfa AF: 0.0531 Hom.: 52

Bravo AF: 0.157

Asia WGS AF: 0.0360 AC: 128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.7
DANN	Benign	0.51
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1870673; hg19: chr12-57199354;