rs12720214

Variant names:

• chr19-10381030-G-C
• rs12720214

Your query was ambiguous. Multiple possible variants found:

• chr19-10381030-G-C
• chr19-10381030-G-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 0.0538 in 151,962 control chromosomes in the GnomAD database, including 266 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 0.054 (266 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0663 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: 0.0538 AC: 8171 AN: 151844 Hom.: 266 Cov.: 31

Gnomad AFR AF: 0.0359

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.0331

Gnomad ASJ AF: 0.0588

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0618

Gnomad FIN AF: 0.0779

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0679

Gnomad OTH AF: 0.0502

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

GnomAD4 genome AF: 0.0538 AC: 8175 AN: 151962 Hom.: 266 Cov.: 31 AF XY: 0.0529 AC XY: 3927 AN XY: 74302

African (AFR) AF: 0.0360 AC: 1491 AN: 41458

American (AMR) AF: 0.0331 AC: 504 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.0588 AC: 204 AN: 3470

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5170

South Asian (SAS) AF: 0.0612 AC: 295 AN: 4820

European-Finnish (FIN) AF: 0.0779 AC: 822 AN: 10550

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0679 AC: 4615 AN: 67952

Other (OTH) AF: 0.0502 AC: 106 AN: 2112

Alfa AF: 0.0600 Hom.: 42

Bravo AF: 0.0503

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.5
DANN	Benign	0.46
PhyloP100		-0.68
PromoterAI		-0.011	Neutral

Splicing

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

Other links and lift over

dbSNP: rs12720214; hg19: chr19-10491706;