rs12870000

Variant names:

• chr13-73355754-A-G
• rs12870000

Your query was ambiguous. Multiple possible variants found:

• chr13-73355754-A-G
• chr13-73355754-A-T

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 0.24 in 152,012 control chromosomes in the GnomAD database, including 4,456 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 0.24 (4456 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 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: 0.240 AC: 36442 AN: 151894 Hom.: 4449 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.240 AC: 36477 AN: 152012 Hom.: 4456 Cov.: 32 AF XY: 0.242 AC XY: 17986 AN XY: 74298

African (AFR) AF: 0.216 AC: 8941 AN: 41480

American (AMR) AF: 0.235 AC: 3595 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 755 AN: 3470

East Asian (EAS) AF: 0.325 AC: 1682 AN: 5168

South Asian (SAS) AF: 0.188 AC: 904 AN: 4816

European-Finnish (FIN) AF: 0.321 AC: 3382 AN: 10550

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16277 AN: 67950

Other (OTH) AF: 0.245 AC: 516 AN: 2110

Alfa AF: 0.237 Hom.: 8560

Bravo AF: 0.237

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.82
DANN	Benign	0.81
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs12870000; hg19: chr13-73929891; COSMIC: COSV69363913;